Phospholipid-derived Fatty Acids Research Articles

Old but not ancient: Rock-leached organic carbon drives groundwater microbiomes.

More than 90% of earth's microbial biomass resides in the continental subsurface, where sedimentary rocks provide the largest source of organic carbon (C). While many studies indicate microbial utilization of fossil C sources, the extent to which rock-organic C is driving microbial activities in aquifers remains largely unknown. Here we incubated oxic and anoxic groundwater with crushed carbonate rocks from the host aquifer and an outcrop rock of the unsaturated zone characterized by higher organic C content, and compared the natural abundance of radiocarbon (14C) of available C pools and microbial biomarkers. The ancient rocks surprisingly released organic substances with up to 72.6±0.3% modern C into the groundwater, suggesting leachable fresh organic material from surface transport was preserved within rock fractures. Over half of the rock-leached compounds were also found in the original groundwater dissolved organic carbon (DOC), indicating in situ release of material stored in rock fractures through weathering processes. In addition to aliphatic and aromatic hydrocarbons, rock-leachates were rich in lipids, peptides, and carbohydrates. Radiocarbon analysis of phospholipid-derived fatty acids showed a rapid microbial response to this 'younger' organic material, comprising up to 31% (anoxic) and 51% (oxic) of their biomass C from the rock-leachate after 18days of incubation. Predictive functional profiling of rock-enriched taxa, including species of Desulfosporosinus, Ferribacterium and Rhodoferax, also suggested metabolic potential for aliphatic and aromatic hydrocarbon degradation. PLFAs of the original groundwater were highly 14C-depleted, indicating utilization of a mixture of fossil and 'younger' C sources. Our findings suggest that carbonate rocks act as temporal sink for 'younger' organic matter, that leaches with fossil hydrocarbons from sedimentary rocks, driving microbial metabolism in subsurface ecosystems.

Nutrient fluxes, oxygen consumption and fatty acid composition from deep-water demo- and hexactinellid sponges from New Zealand

Sponges are an important component of deep-water ecosystems enhancing eukaryotic biodiversity by hosting diverse endo- and epibiota and providing three dimensional habitats for benthic invertebrates and fishes. As holobionts they are important hosts of microorganisms which are involved in carbon and nitrogen cycling. While increasing exploration of deep-water habitats results in new sponge species being discovered, little is known about their physiology and role in nutrient fluxes. Around New Zealand (Southwest Pacific), the sponge biodiversity is particularly high, and we selected six deep-sea sponge genera (Saccocalyx, Suberites, Tedania, Halichondria/Dendoricella, Lissodendoryx) and a member of the Sceptrulophora order for in-situ and ex-situ experiments.We investigated the biochemical composition of the sponges, measured oxygen consumption and inorganic nutrient fluxes, as well as bacterial and phospholipid-derived fatty acid (PLFA) compositions. Our aim was to assess differences in fluxes and fatty acid composition among sponges and linking their bacterial communities to nitrogen cycling processes.All sponges excreted nitrite and ammonia. Nitrate and phosphate excretion were independent of phylum affiliation (Demospongiae, Hexactinellida). Nitrate was excreted by Halichondria/Dendoricella and Lissodendoryx, whereas Suberites, Tedania, and Sceptrulophora consumed it. Phosphate was excreted by Sceptrulophora and Halichondria/Dendoricella and consumed by all other sponges. Oxygen consumption rates ranged from 0.17 to 3.56 ± 0.60 mmol O2 g C-1 d−1.The PLFA composition was very sponge-genera dependent and consisted mostly of long-chain fatty acids. Most PLFAs were sponge-specific, followed by bacteria-specific PLFAs, and others.All sponges, except for Suberites, were low-microbial abundance (LMA) sponges whose bacterial community composition was dominated by Proteobacteria, Bacteroidota, Planctomycetota, and Nitrospinota. Suberites consisted of high-microbial abundance (HMA) sponges with Proteobacteria, Chloroflexota, Acidobacteriota, and Actinobacteriota as dominant bacteria.Based on the inorganic nitrogen flux measurements, we identified three types of nitrogen cycling in the sponges: In type 1, sponges (Dendoricella spp. indet., Lissodendoryx) respired aerobically and ammonificated organic matter (OM) to ammonium, fixed N2 to ammonium, and nitrified aerobically heterotrophically produced ammonium to nitrate and nitrite. In type 2, sponges (Halichondria sp., Sceptrulophora, Suberites, Tedania) respired OM aerobically and ammonificated it to ammonium. They also reduced nitrate anaerobically to ammonium via dissimilatory nitrate reduction to ammonium. In type 3, ammonium was microbially nitrified to nitrite and afterwards to nitrate presumably by ammonium-oxidizing Bacteria and/or Archaea.

The potential of soil microbial communities to transform deoxynivalenol in agricultural soils—a soil microcosm study

Infestation of cereal fields with toxigenic Fusarium species is identified as an environmental source for the mycotoxin deoxynivalenol (DON). During rain events, DON may be washed off from infested plants and enter the soil, where microbial transformation may occur. Although some studies showed DON transformation potential of soil microbial communities in liquid soil extracts, these findings can not be transferred to environmental conditions. Accordingly, microbial transformation of DON in soil has to be investigated under realistic conditions, e.g., microcosms mimicking field situations. In this study, we investigated the potential of soil microbial communities to transform DON in six different agricultural soils at two levels (0.5 and 5 µg g–1). The dissipation and the formation of transformation products were investigated in a period of 35 days and compared to a sterilized control. In addition, we measured soil respiration and applied the phospholipid-derived fatty acid (PLFA) analysis to assess whether soil microbial community characteristics are related to the microbial transformation potential. Dissipation of DON in non-sterilized soils was fast (50% dissipation within 0.6–3.7 days) compared to the sterile control where almost no dissipation was observed. Thus, dissipation was mainly attributed to microbial transformation. We verified that small amounts of DON are transformed to 3-keto-deoxynivalenol (3-keto-DON) and 3-epi-deoxynivalenol (3-epi-DON), which were not detectable after 16-day incubation, indicating further transformation processes. There was a trend towards faster transformation in soils with active and large microbial communities and low fungi-to-bacteria ratio.

Variations in Soil Organic Carbon Fractions and Microbial Community in Rice Fields under an Integrated Cropping System

Combining rice cultivation and aquaculture into an integrated cropping system is a management approach that enhances the sustainability of rice fields. However, how soil characteristics influence soil microbial community characteristics following implementation of such an integrated system, particularly in the waterlogged paddies of the Pearl River Delta, is poorly understood. An integrated cropping system (rice–fish–duck integrated cropping system, RFD) and a rice–pepper rotation system (RPS) were compared using a conventional rice cropping system (CRS) as a reference. We used phospholipid-derived fatty acid (PLFA) analysis to assess soil microbial community structure and function and measured soil nutrient content and organic carbon fractions. Our results indicated that the soil nutrient content, organic carbon fractions, and C-hydrolyzing activities differed among the cropping systems. The RFD resulted in higher microbial PLFA concentrations and a lower ratio of Gram-positive to Gram-negative bacteria than CRS. Additionally, the integrated system reduced microbial nutrient stress by increasing soil pH. Further analysis revealed that active soil organic carbon significantly affected the soil microbial community. Thus, the RFD integrated cropping systems that alter the combined actions of pH and active organic carbon fractions can be used to improve soil microbial communities.

Molecular Approaches in Soil Microbial Analysis: Forensic Perspective

The growing field of soil microbial forensics provides the legal answer to how microorganisms play a crucial role in criminal investigations. It is an advanced crossdisciplinary science capable of offering significant physical evidence with considerable interest in criminal investigations, environmental crime, and counterterrorism. Microbial forensics of soil consists of different techniques to identify and evaluate microbial abundance, their complexity, and their interaction with soil and surrounding objects. The present review highlights various microbial analysis techniques such as Terminal restriction fragment length polymorphism, Temperature/Denaturing Gradient Gel Electrophoresis, Amplified Ribosomal DNA Restriction Analysis, Length Heterogeneity PCR, Phospholipid-derived fatty acids, Fluorescence in situ hybridization, Stable-isotope probing and metagenomics using nextgeneration sequencing. This article also summarises the challenges faced in soil microbial forensics, various statistical approaches, reference databases commonly used in forensic soil studies, and different methodological approaches used in forensic laboratories. Literature was studied using various online bibliographic databases like Google Scholar, Web of Science, Pub Med, Scopus, and several other search engines. Conclusive evidence generated by this paper signifies the importance of soil microbes to assist forensic scientists and researchers in selecting adequate methods to differentiate soil samples. The present comparative study concluded that targeted molecular analysis of microbes as a forensic soil typing tool has a lot of potential and should be investigated further.

Prolonged drought causes negative plant-soil feedbacks in grassland species under field conditions

Climate change has been shown to alter plant-soil feedbacks (PSFs, the impacts of plants on future communities via their impacts on soil biotic and abiotic properties), with implications for plant community dynamics. However, few studies have assessed effects on PSFs under field conditions or the mechanisms involved. We assessed drought effects on PSFs of four common grassland species (Lolium multiflorum, Medicago sativa, Plantago lanceolata, and Trifolium repens) in situ in a mesic grassland under ambient rainfall and prolonged drought conditions using a long-term rainfall manipulation system. The four species were first grown in monocultures in sub-plots of each of six ambient and drought plots to condition the soils. Then, each species was grown in a sub-plot conditioned by the same species (‘home’) and a sub-plot conditioned by each of the other three species (‘away’). We found that three species (L. multiflorum, M. sativa and T. repens) produced higher biomass in their ‘home’ soil than away soil under ambient rainfall while they consistently grew better in away soil under drought conditions, indicating drought-induced negative shifts in PSFs. There were strong interaction effects of rainfall treatment and conditioning species on several phospholipid-derived fatty acids markers, including a marker associated with arbuscular mycorrhizal fungi (AMF). We found a significant positive correlation between PSFs and the AMF marker across all treatment combinations, indicating that PSFs were driven by changes in positive plant-soil biotic interactions. Furthermore, drought increased plant parasitic nematode abundances. We found a strong significant negative correlation between PSFs and plant parasitic nematodes across all treatment combinations, indicating that the drought-induced shifts to more negative PSFs were driven by increased negative plant-soil biotic interactions. Drought may therefore negatively impact common grassland species due to stronger negative PSFs but at the same time promote species co-existence by reducing the abundance of competitive species.

Effects of a bionematicide 1,4-naphthoquinone solution on soil microbial community assessed by PLFA: Tracing toxicity indicators

The worldwide demand on bionematicides is in a growing trend, fueled by environmental concerns with potential negative impacts of synthetic products on ecosystems and non-target organisms, as well as by the need to provide solutions to organic farming management. As such, the main goal of the present study was to evaluate the impact of 1,4-naphthoquinone (NTQ), a nematicidal compound found in natural products such as walnut husk, on soil microbial community (non-target organisms), and determine ecotoxicological indicators in order to follow and quantify the effect of this compound. The effects on diversity and metabolic state of the microbial community were evaluated using a Phospholipid-derived Fatty Acid analysis (PLFA) method. Tests were conducted on a natural uncontaminated soil spiked with a range of NTQ concentrations (up to 768 mg/kg), as well as comparable control solutions containing solubilization enhancer Triton X-100 (TX100). NTQ impacted the soil microbial community, causing significant changes on global PLFA profile at 12 mg/kg, and significant changes on taxonomic biomarker balance at 96 mg/kg. TX100 also caused a significant effect on the global profile, but only at 192 mg/kg NTQ-equivalent. The modifications brought by either compounds were distinct, as different indicators were affected. The effects of NTQ on microbial community were quantifiable for several indicators by calculating half maximal effective concentrations (EC50). The method used proved to be suitable for the assessment of NTQ ecotoxicity in soils.

Soil health indicators and crop yield in response to long-term cropping sequence and nitrogen fertilization

There is a need for including soil physical and biological properties along with chemical properties to accurately measure soil health and relate to crop yields. The objective of this study was to determine a suite of soil health indicators that were sensitive to cropping systems and N fertilization and relate to soil properties and dryland crop yield in a 14-yr-old cropping sequence and N fertilization study in eastern Montana, USA. Main-plot (cropping sequence) treatments were conventional till barley (Hordeum vulgaris L.)/spring wheat (Triticum aestivum L.)-fallow (CTWF), no-till continuous barley/spring wheat (NTCW), no-till barley/spring wheat-fallow (NTWF), and no-till barley/spring wheat-pea (Pisum sativum L.) (NTWP) and split-plot (N fertilization) treatments were 0 (N0) and 80/100 kg N ha−1 (N1) applied to barley and spring wheat. Barley was grown for the first six years that was replaced by spring wheat for the last eight years. The NTCW increased aggregate stability, wet aggregate stability index, average slake aggregate, P concentration, KMNO4-extractable C, CO2 flush (1 d incubation), potentially mineralizable N, and N-acetyl β-glucosaminidase (NAG), but reduced NO3-N concentration compared to other treatments. Water-stable aggregation, macro-porosity, volumetric water content at water saturation, and Mg concentration were greater with N0, but water-extractable total N and NO3-N concentration were greater with N1. Mean crop (barley/spring wheat) yield from 2006 to 2019 were greater in NTCW with N1 than other treatments. Multivariate analysis showed that phospholipid-derived fatty acid (PLFA) and CO2 flush at 4-d incubation were negatively related to Ca and Al concentrations, but positively to crop yield. Microbial abundance and activity can be used as important soil health indicators that were enhanced by no-tillage with increased cropping intensity and related to crop yield.

Flood Pulse Irrigation of Meadows Shapes Soil Chemical and Microbial Parameters More Than Mineral Fertilization

While mineral fertilization increases agricultural yields, it also bears the risk of contaminating non-target ecosystems and negatively affecting soil chemical parameters and microbial communities. This calls for alternative and more sustainable agricultural practices that reduce the use of fertilizers. Flood pulse irrigation could be an alternative to mineral fertilization of hay meadows, since it increases the yield with little or no application of fertilizer. However, the positive and negative implications of flood pulse irrigation on soil chemical parameters and particularly soil microbial communities are still largely unknown. In this study, we assessed shifts in soil microbial communities (SMC) as a response to changes in soil chemical parameters after flood pulse irrigation and/or fertilization of meadows. We determined soil chemical (Corg, Ntot, water extractable N, P, K, pH) and microbial (phospholipid-derived fatty acids, PLFA) parameters of 12 meadows in a 2 × 2 factorial design, comprising flood pulse irrigation and fertilization. Corg, Ntot, and water content as well as microbial biomass were higher in flood-irrigated than in non-flooded soils. Soil microbial biomass positively correlated with Corg, Ntot, and water extractable N. Gram-negative bacteria significantly increased, whereas the fungi/bacteria ratio significantly decreased in flood-irrigated soils compared to non-flooded soils. Arbuscular mycorrhizal fungi were positively correlated with soil pH. Flood pulse irrigation seemed to promote the build-up of a larger soil carbon and nitrogen pool as well as higher water content and microbial biomass. By this, it potentially mitigated negative mineral fertilization effects such as changed soil pH and reduced carbon use efficiency. We conclude that flood pulse irrigation may represent a sustainable alternative to mineral fertilization.

The benefits of the no-till system on soil health and crop yields in dryland cropping systems

Context The no-till (NT) system is used to control soil erosion and nutrient losses, but extensive evaluation of NT on soil health and long-term crop yields compared to conventional till (CT) is needed to evaluate the overall benefit of NT. Aims The objective of this study was to compare NT and CT on soil health and long-term crop yields in two dryland farming sites in the northern Great Plains, USA. Methods Soil samples collected from two long-term (14- and 36-years-old) experiments of dryland farming under NT and CT continuous spring wheat (Triticum aestivum L.) and barley (Hordeum vulgaris L.)/spring wheat-fallow rotation were analysed for 66 soil physical, chemical, biological and biochemical properties and crop yields determined. Key results NT increased wet soil stability index, average slake aggregate and total shrinkage by 12–61%, but reduced saturated hydraulic conductivity by 24–31% compared to CT. Soil Al, Ba, Cu and S concentrations were 10–16% greater, but electrical conductivity, Co, Na and Zn concentrations, and Na-absorption ratio were 9–33% lower with NT than CT. Similarly, NH4-N concentration, CO2 evolution, phospholipid-derived fatty acid (PLFA), phosphomonoesterase and arysulfatase were 13–38% greater, but water extractable N, NO3-N concentration and potential N mineralisation were 16–31% lower with NT than CT. Mean crop yield across years were similar between NT than CT. Conclusions NT can enhance overall soil health and sustain dryland crop yields compared to CT in the northern Great Plains, USA. Implications Long-term sustainability of dryland cropping system can be maintained by using the NT system.

Endolithic Microbial Carbon Cycling in East Antarctica.

Antarctica is an ideal analogue for studying the limits of life. Despite severe temperature fluctuations and desiccating conditions, life is commonly found colonizing the structural cavities within Antarctic rocks (i.e., endoliths). Previous studies have speculated that the slow cycling of endoliths in the McMurdo Dry Valleys may be the limit of life on Earth. However, very little is known about the in situ activities of these communities-especially in regions outside the McMurdo Dry Valleys where endoliths are thought to be cycling carbon very slowly (e.g., hundreds of years). Here, we show that East Antarctic endoliths found on nunataks are cycling carbon quickly and are therefore quite active. Through radiocarbon (14C) analyses of the viable cell membrane (as phospholipid-derived fatty acids [PLFA]), we found that the Δ14C composition of these microbial communities was on average predominantly modern, with a few samples signaling older carbon in the system. These findings indicate that endoliths inhabiting inland Antarctic nunataks are cycling carbon on decadal timescales, which support the notion that endoliths in Antarctica are cycling carbon quickly. This work provides new insights into the potential variability of Antarctic endolith activities and demonstrates that, despite the climatic extremes that exist farther inland on the most inhospitable continent on Earth, indigenous life can thrive.

Differential processing of dissolved and particulate organic matter by deep-sea sponges and their microbial symbionts

Deep-sea sponges create hotspots of biodiversity and biological activity in the otherwise barren deep-sea. However, it remains elusive how sponge hosts and their microbial symbionts acquire and process food in these food-limited environments. Therefore, we traced the processing (i.e. assimilation and respiration) of 13C- and 15N-enriched dissolved organic matter (DOM) and bacteria by three dominant North Atlantic deep-sea sponges: the high microbial abundance (HMA) demosponge Geodia barretti, the low microbial abundance (LMA) demosponge Hymedesmia paupertas, and the LMA hexactinellid Vazella pourtalesii. We also assessed the assimilation of both food sources into sponge- and bacteria-specific phospholipid-derived fatty acid (PLFA) biomarkers. All sponges were capable of assimilating DOM as well as bacteria. However, processing of the two food sources differed considerably between the tested species: the DOM assimilation-to-respiration efficiency was highest for the HMA sponge, yet uptake rates were 4–5 times lower compared to LMA sponges. In contrast, bacteria were assimilated most efficiently and at the highest rate by the hexactinellid compared to the demosponges. Our results indicate that phylogeny and functional traits (e.g., abundance of microbial symbionts, morphology) influence food preferences and diet composition of sponges, which further helps to understand their role as key ecosystem engineers of deep-sea habitats.

Cover cropping enhances soil microbial biomass and affects microbial community structure: A meta-analysis

Cover crops have been increasingly grown for improving soil health and crop production and minimizing environmental impact compared to no cover crop. Systematic documentation of cover cropping effects on soil microbial abundance and community structure, however, is scarce. A meta-analysis including data from 81 available studies was conducted to elucidate the effect of “cover crop” versus “no cover crop” on soil microbial community abundance and structure. Microbial biomass C and N (MBC and MBN) and total phospholipid-derived fatty acids (PLFA) were taken as proxies for soil microbial abundance, and total fungi, total bacteria, gram-positive and -negative bacteria, actinomycete, and arbuscular mycorrhizal fungi (AMF) for microbial community structure. Compared to no cover crop, cover crop overall enhanced PLFA, MBC, and MBN by 24, 40, and 51%, respectively. Soil total bacteria and total fungi, and the groups in them increased by 7–31% with cove crop compared to no cover crop. Fungi were affected more by cover crop than bacteria as indicated by the greater fungi/bacteria ratio. In depth categorical meta-analyses revealed that the legume and nonlegume cover crop mixture reduced MBC, PLFA, and actinomycete compared to legume or nonlegume cover crop alone. Legume cover crop enhanced actinomycete in comparison to nonlegume or the cover crop mixture. Incorporation of cover crop residue into the soil increased PLFA, total bacteria, AMF root colonization, and spore density, but decreased gram-positive and -negative bacteria and AMF compared to residue placed at the surface or removed from the soil. Microbial parameters due to cover crop compared to no cover crop were related to soil properties and annual precipitation. Medium-textured soils showed greater response of cover crop on PLFA, total bacteria and fungi, and actinomycete than fine- or coarse-textured soils. We conclude that cover crops enhance soil microbial community biomass and affected community structure compared to no cover crop and the responses of microbial parameters to cover crop varied with soil and climatic conditions. Cover crops can enhance biological soil health by enhancing microbial community abundance compared to no cover crop.

A Cross-System Comparison of Dark Carbon Fixation in Coastal Sediments.

Dark carbon fixation (DCF) by chemoautotrophic microorganisms can sustain food webs in the seafloor by local production of organic matter independent of photosynthesis. The process has received considerable attention in deep sea systems, such as hydrothermal vents, but the regulation, depth distribution, and global importance of coastal sedimentary DCF have not been systematically investigated. Here we surveyed eight coastal sediments by means of stable isotope probing (13C‐DIC) combined with bacterial biomarkers (phospholipid‐derived fatty acids) and compiled additional rates from literature into a global database. DCF rates in coastal sediments range from 0.07 to 36.30 mmol C m−2 day−1, and there is a linear relation between DCF and water depth. The CO2 fixation ratio (DCF/CO2 respired) also shows a trend with water depth, decreasing from 0.09 in nearshore environments to 0.04 in continental shelf sediments. Five types of depth distributions of chemoautotrophic activity are identified based on the mode of pore water transport (advective, bioturbated, and diffusive) and the dominant pathway of microbial sulfur oxidation. Extrapolated to the global coastal ocean, we estimate a DCF rate of 0.04 to 0.06 Pg C year−1, which is less than previous estimates based on indirect measurements (0.15 Pg C year−1), but remains substantially higher than the global DCF rate at deep sea hydrothermal vents (0.001–0.002 Pg C year−1).

Dark CO2 fixation into phospholipid-derived fatty acids by the cold-water coral associated sponge Hymedesmia (Stylopus) coriacea (Tisler Reef, NE Skagerrak)

ABSTRACTMany cold-water sponges harbour microorganisms of which the role in the sponge host remains enigmatic. Here, we show a transfer of fixed inorganic carbon by sponge-associated microbes to its host, the cold-water coral encrusting sponge Hymedesmia (Stylopus) coriacea. Sponge were collected at approx. 100 m depth and incubated for 1.5–2.5 days with 13C labelled dissolved inorganic carbon (DIC) as tracer. Total DIC fixation rates ranged from 0.03–0.11 mmol C × mmol Csponge × d−1. 13C-tracer was recovered in bacterial-specific (i.e. short and branched) and sponge-specific (very long-chained) phospholipid-derived fatty acids (PLFA's), but was not incorporated into archaeal lipids. 13C-incorporation in biomarkers such as C16:1w7c and C18:1w7c indicated that nitrifying and/or sulphur-oxidizing bacteria (chemoautotrophs) were likely active in the sponge. Trophic transfer of microbially-fixed carbon to the sponge host was confirmed by recovery of label in very long chain fatty acids (VLCFA's) including C26:2 and C26:3. Tracer accumulation into several VLCFA's continued after removal of 13C-DIC, while tracer in most bacteria-specific PLFA's declined, indicating a transfer and elongation of bacterial-specific PLFA's to sponge-specific PLFA's. This implies that PLFA precursors released from chemo- as well as heterotrophic microbes in sponges contributed to the synthesis of VLCFA's, identifying sponge-associated bacteria as symbionts of the sponge.

Sources of carbon isotopes in Baltic Sea sediments

Radiocarbon and specific phospholipid-derived biomarkers were used to trace chemical warfare agents (CWA) at the Gotland Deep dumping site of chemical weapons. Δ14C measurements in different classes of organic fractions, such as total lipid extracts (TLE), humic acids (HA) and phospholipid-derived fatty acids (PLFA) isolated from bottom sediments have been applied. In addition, specific PLFA biomarkers extracted from sediments were analyzed by gas chromatography. Contrary to Δ14CHA, the most depleted Δ14CTOC and Δ14CTLE values were found in bottom sediments samples collected at the CWA dumpsite, which were attributed to different carbon sources.

Potentials and limitations of quantification of fungi in freshwater environments based on PLFA profiles

Aquatic fungi are increasingly recognized for their contribution to carbon cycling in aquatic ecosystems, both as saprotrophs and parasites. Their quantification in mixed communities is crucial to assess their ecological significance but remains challenging. We characterized the phospholipid-derived fatty acid (PLFA) composition of fifteen aquatic fungal isolates from Chytridiomycota (chytrids) and Dikarya. Additionally, we identified PLFA patterns of chytrids infecting phytoplankton and their zoospores. PLFA composition of zoospores was highly similar among different taxa, but were distinct from their respective sporangial life-stage. Finally, we applied a fatty acid-based Bayesian mixed model (FASTAR) and tested its potential to quantify fungi in complex mixtures with bacteria and phytoplankton using PLFA profiles. While the quantification of chytrid biomass in low quantities was rather imprecise, the model predicted the contribution of filamentous fungi and other components with fair accuracy, supporting the suitability of this approach to quantify fungal biomass in aquatic environments. • PLFA patterns of fungi can be applied to quantify them in mixed aquatic communities. • Zoospores and sporangia of Chytridiomycota differ in their PLFA patterns. • PLFA patterns of phytoplankton infected by fungal parasites change significantly. • Quantifying aquatic fungi with a Bayesian mixed model based on PLFA is generally recommended. • Quantification of Chytridiomycota based on PLFA patterns remains difficult.

Biodegradation and photooxidation of phenolic compounds in soil—A compound-specific stable isotope approach

Phenolic compounds occur in a variety of plants and can be used as model compounds for investigating the fate of organic wastewater, lignin, or soil organic matter in the environment. The aim of this study was to better understand and differentiate mechanisms associated with photo- and biodegradation of tyrosol, vanillin, vanillic acid, and coumaric acid in soil. In a 29 d incubation experiment, soil spiked with these phenolic compounds was either subjected to UV irradiation under sterile conditions or to the native soil microbial community in the dark. Changes in the isotopic composition (δ13C) of phenolic compounds were determined by gas chromatography–isotope ratio mass spectrometry and complemented by concentration measurements. Phospholipid-derived fatty acid and ergosterol biomarkers together with soil water repellency measurements provided information on soil microbial and physical properties. Biodegradation followed pseudo-first-order dissipation kinetics, enriched remaining phenolic compounds in 13C, and was associated with increased fungal rather than bacterial biomarkers. Growing mycelia rendered the soil slightly water repellent. High sample variation limited the reliable estimation of apparent kinetic isotope effects (AKIEs) to tyrosol. The AKIE of tyrosol biodegradation was 1.007 ± 0.002. Photooxidation kinetics were of pseudo-zero- or first-order with an AKIE of 1.02 ± 0.01 for tyrosol, suggesting a hydroxyl-radical mediated degradation process. Further research needs to address δ13C variation among sample replicates potentially originating from heterogeneous reaction spaces in soil. Here, nuclear magnetic resonance or nanoscopic imaging could help to better understand the distribution of organic compounds and their transformation in the soil matrix.

Pethoxamid dissipation and microbial activity and structure in an agricultural soil: Effect of herbicide rate and organic residues

Soil is a non-renewable resource, and its degradation compromises human health, natural ecosystems, and even the climate. The application of organic amendments and herbicides is commonplace in agriculture, and their impact on soil fertility needs to be evaluated. Therefore, the objective was to evaluate the effect on soil microbial activity and structure of amendments, sewage sludge (SS) and green compost (GC), and the rate of herbicide pethoxamid applied (2, 10 and 50 mg kg−1). Herbicide dissipation kinetics, soil dehydrogenase activity (DHA) and the profile of phospholipid-derived fatty acids (PLFAs) extracted from the soil have been determined in unamended (S) and amended (S + SS and S + GC) soils. The dissipation curves of pethoxamid applied at the three rates closely fitted a single first order kinetics model in all the soils. The dissipation rate decreased with the rate applied in the order 2 mg kg−1 > 10 mg kg−1 > 50 mg kg−1 in unamended and amended soils. However, the half-life or time required for 50% dissipation (DT50) of pethoxamid was not significantly different in unamended and amended soils when applied at 2 and 10 mg kg−1, but it was lower in the amended soils than in the unamended one when the herbicide was applied at the highest rate. The highest DHA mean values were obtained in S + GC treated with pethoxamid at 2, 10 and 50 mg kg−1; however, DHA was lower in S + SS than in S. Peak DHA values were observed in S and S + GC soils treated with pethoxamid at 2 mg kg−1 at 15 days of incubation, and in S, S + GC and S + SS treated with the herbicide at 10 and 50 mg kg−1 at 35 days of incubation. These peak DHA values are close to 50% of herbicide dissipation. A statistical analysis of the PLFA results has revealed significant effects for sampling time in all the soils, for the pethoxamid rate, and for the interaction between time and pethoxamid rate only in S + GC and S + SS. The application of organic amendments to soil accelerated the dissipation of higher rates of pethoxamid compared to the unamended soil, which is important to prevent the herbicide's negative impacts on the soil microbial community.

Chemical Amendments of Dryland Saline–Sodic Soils Did Not Enhance Productivity and Soil Health in Fields without Effective Drainage

Core IdeasThe amount of land impacted by salinity or sodicity is increasing worldwide.Precision conservation can be used to target corrective treatments to problem areas.Chemical amendments did not enhance soil health or plant productivity in northern Great Plains soils that did not have effective drainage systems.The application of chemical amendments as preventative treatment in tile drained North America northern Great Plains fields did not improve soil health (water infiltration and microbial diversity) and either reduced or did not increase crop yields.These results were partially attributed to high subsoil bulk densities and low drainable porosities.A common restoration treatment for saline–sodic soils involves improving soil drainage, applying soil amendments (e.g., CaSO4, CaCl2, or elemental S), and leaching with water that has a relatively low electrical conductivity. However, due to high subsoil bulk densities and low drainable porosities, these treatments many not be effective in glaciated dryland systems. A 3‐yr field study conducted in three model systems determined the impact of chemical amendments (none, CaCl2, CaSO4, and elemental S) on plant growth, microbial composition, temporal changes in electrical conductivity (ECe), and the relative sodium content (%Na). Chemical amendments (i) either reduced or did not increase maize (Zea mays), soybean (Glycine max), and sorghum (Sorghum bicolor) yields; (ii) did not increase water infiltration or microbial biomass as determined using the phospholipid‐derived fatty acid (PLFA) technique; and (iii) did not reduce ECeor %Na. These results were attributed to high bulk densities and low drainable porosities that reducing the drainage effectiveness in the model backslope and footslope soils, the presence of subsurface marine sediments that provided a source for sodium and other salts that could be transported through capillary action to the surface soil, high sulfate and gypsum contents in the surface soil, and relatively low microbial biomass values. The results suggests that an alternative multistep saline sodic soil restoration approach that involves increasing exchangeable Ca+2through enhanced microbial and root respiration and increasing transpiration and soil drainage by seeding full season deep rooted perennial vegetation should be tested.