Phospholipid fatty acid profiling of microbial communities-a review of interpretations and recent applications

Evaluation of simplified ester-linked fatty acid analysis (ELFA) for phospholipid fatty acid (PLFA) analysis of bacterial population

Phospholipid fatty acid (PLFA) analysis is used for characterizing microbial communities based on their lipid profiles. This method avoids biases from PCR or culture, allowing data collection in a natural state. However, PLFA is labor-intensive due to lipid fractionation. Simplified ester-linked fatty acid analysis (ELFA), which skips lipid fractionation, offers an alternative. It utilizes base-catalyzed methylation to derivatize only lipids, not free fatty acids, and found glycolipid and neutral lipid fractions are scarcely present in most bacteria, allowing lipid fractionation to be skipped. ELFA method showed a high correlation to PLFA data (r = 0.99) and higher sensitivity than the PLFA method by 1.5-2.57-fold, mainly due to the higher recovery of lipids, which was 1.5-1.9 times higher than with PLFA. The theoretical limit of detection (LOD) and limit of quantification (LOQ) for the ELFA method indicated that 1.54-fold less sample was needed for analysis than with the PLFA method. Our analysis of three bacterial cultures and a simulated consortium revealed the effectiveness of the ELFA method by its simple procedure and enhanced sensitivity for detecting strain-specific markers, which were not detected in PLFA analysis. Overall, this method could be easily used for the population analysis of synthetic consortia.

Selenium availability in tea: Unraveling the role of microbiota assembly and functions

Tea (Camellia sinensis (L.) O. Kuntze) plants have a strong ability to accumulate selenium (Se). However, the question of how tea plants affect Se availability has received little attention. In this study, five tea cultivars, including Soubei (SB), Aolǜ (AL), Longjing43 (LJ), Zhaori (ZR) and Fenglǜ (FL), were chosen for the study. Quantitative Microbial Ecology Chip and high-throughput sequencing were used to explore the effects of five tea cultivars on soil functions, microbial community structures and Se availability. The results showed that the total soil Se content in the FL garden was lower compared to LJ and SB gardens, whereas available Se was highest in the FL garden. Based on the Bray-Curtis distances, tea cultivar was the main factor affecting bacterial and fungal community structures. The abundance of functional genes concerning carbon, nitrogen, phosphorus and sulfur cycling processes varied among tea gardens. The higher soil NH4+ and NO3- contents, and higher abundance of functional genes like nifH, amoA1 and narG, whereas lower total nitrogen in the FL garden than in the AL and LJ tea gardens demonstrated that the FL tea plants induced microbes to accelerate soil nitrogen cycling processes. Dominant microbes that positively related with functional genes like nifH, narG, and amoA1 were also positively related with the available Se content. In conclusion, tea cultivars could regulate soil functions through affecting microbial community structures and then affecting the soil Se availability. The soil nitrogen cycle processes are suggested to be closely related with Se transformation in tea gardens.

Beyond the rootzone: Unveiling soil property and biota gradients around plants

Although the effects of plants on soil properties are well known, the effects of distance from plant roots to root-free soil on soil properties and associated soil organisms are much less studied. Previous research on the effects of distance from a plant explored specific soil organisms and properties, however, comparative studies across a wide range of plant-associated organisms and multiple model systems are lacking. We conducted a controlled greenhouse experiment using soil from two contrasting habitats. Within each soil type, we cultivated two plant species, individually and in combination, studying soil organisms and properties in the root centre, the root periphery, and the root-free zones. We showed that the distance from the cultivated plant (representing decreasing amount of plant roots) had a significant impact on the abiotic properties of the soil (pH and available P and N) and also on the composition of the fungal, bacterial, and nematode communities. The specific patterns, however, did not always match our expectations. For example, there was no significant relationship between the abundance of fungal pathogens and the distance from the cultivated plant compared to a strong decrease in the abundance of arbuscular mycorrhizal fungi. Changes in soil chemistry along the distance from the cultivated plant were probably one of the important drivers that affected bacterial communities. The abundance of nematodes also decreased with distance from the cultivated plant, and the rate of their responses reflected the distribution of their food sources. The patterns of soil changes along the gradient from plant to root-free soil were largely similar in two contrasting soil types and four plant species or their mixtures. This suggests that our results can be generalised to other systems and contribute to a better understanding of the mechanisms of soil legacy formation.

A Treasure Trove of Urban Microbial Diversity: Community and Diversity Characteristics of Urban Ancient Ginkgo biloba Rhizosphere Microorganisms in Shanghai

Rapid urbanization has exerted immense pressure on urban environments, severely constraining the growth of ancient trees. The growth of ancient trees is closely linked to the microbial communities in their rhizospheres, and studying their community characteristics may provide new insights into promoting the growth and rejuvenation of ancient trees. In this study, the rhizosphere soil and root systems of ancient Ginkgo biloba trees (approximately 200 years old) and adult G. biloba trees (approximately 50 years old) in Shanghai were selected as research subjects. Phospholipid fatty acid (PLFA) analysis and high-throughput sequencing were employed to investigate the diversity of microbial communities in the G. biloba rhizosphere. The results indicated that the 19 PLFA species selected to characterize the soil microbial community structure and biomass were present in the rhizosphere soil of both ancient and adult G. biloba trees. However, the total microbial biomass and the microbial biomass in the rhizosphere soil of ancient G. biloba were lower than the microbial biomass in the rhizosphere soil of adult G. biloba. The biomasses of Gram-negative bacteria (G-), arbuscular mycorrhizal fungi (AMF), and protozoans (P) were significantly different. Total phosphorus, organic matter, and pH may be the key factors influencing the soil microbial community in the rhizosphere zone of ancient G. biloba. An in-depth study of AMF showed that the roots and rhizosphere soil of G. biloba contained abundant AMF resources, which were assigned to 224 virtual taxa using the MaarjAM reference database, belonging to four orders, ten families, and nineteen genera. The first and second most dominant genera were Glomus and Paraglomus, respectively. Archaeospora and Ambispora were more dominant in the rhizosphere than the roots. Furthermore, the abundance of live AMF was significantly higher in ancient G. biloba than in adult G. biloba. Therefore, future research should focus on the improvement of soil environmental characteristics and the identification and cultivation of indigenous dominant AMF in the rhizosphere of ancient G. biloba, aiming for their effective application in the rejuvenation of ancient trees.

Enzyme stoichiometry reveals microbial nitrogen limitation in stony soils

Resource limitation for soil microorganisms is the crucial factor in nutrient cycling and vegetation development, which are especially important in arid climate. Given that rock fragments strongly impact hydrologic and geochemical processes in arid areas, we hypothesized that microbial resource (C and N) limitation will increase along the rock fragment content (RFC) gradient. We conducted a field experiment in Minjiang river arid valleys with four RFC content (0 %, 25 %, 50 %, and 75 %, V V-1) and four vegetation types (Artemisia vestita, Bauhinia brachycarpa, Sophora davidii, and the soil without plants). Activities of C (β-1,4-glucosidase, BG), N (β-1,4-N-acetyl-glucosaminidase, NAG; L-leucine aminopeptidase, LAP), and P (acid phosphatase, ACP) acquiring enzymes were investigated to assess the limitations by C, N or P. In unplanted soil, the C acquiring enzyme activity decreased by 43 %, but N acquiring enzyme activity increased by 72 % in 75 % RFC than those in rock-free soils (0 % RFC). Increasing RFC reduced C:N and C:P enzymatic ratios, as well as vector length and vector angle (< 45°). Plants increased the activities of C and N acquiring enzymes in soils, as well as C:P and N:P enzyme activities, as well as vector length (by 5.6 %-25 %), but decreased vector angle (by 13 %-21 %). Enzyme stoichiometry was dependent on biotic and abiotic factors, such as soil water content, soil C:N, and total content of phospholipid fatty acids, reflecting microbial biomass content. Increased RFC shifted enzymatic stoichiometry toward lower C but stronger N limitation for microorganisms. Vegetation increased microbial C and N limitation, and impacted the enzymatic activities and stoichiometry depending on shrub functional groups. Consequently, the direct effects of vegetation, nutrient availability and microbial biomass content, as well as indirect effects of soil properties collectively increased microbial resource limitations along the RFC gradient.

Eisenia fetida-driven vermitechnology for the eco-friendly transformation of steel waste slag into organic amendment: An insight through microbial diversity and multi-model approach

The processing of steel waste slag from the black metallurgical sector seriously threatened the ecology. To counter these dangers, appropriate detoxification methods were required. Vermitechnology was one such strategy that could successfully convert this industrial waste into nutrient-rich products suitable for use in agriculture. This research primarily focuses on employing vermitechnology for the transformation of waste steel slag into vermicompost and to determine changes in microbial composition, nutrient cycling, and metal detoxification facilitated by earthworms (Eisenia fetida). Earthworm populations in steel waste vermibeds (sw-vermibeds) increased by 2.87-3.07 folds. T1(SW + CD-1:1) comparatively showed increased levels of nutrients such as nitrogen, phosphorus, and potassium. Microbial and enzymatic parameters were more pronounced in treatment T1. The findings of phospholipid fatty acid (PLFA) diversity demonstrate microbial diversity and fatty acid composition. Based on PLFA Sobol Sensitivity Analysis (SSA), PUFA and cyclo were the most sensitive inputs to the presence of heavy metal (HMs) concentrations in SW. In accordance with Taylor-based modelling, R-tree, and Mars were the most trusted regression models for predicting HMs toxicity on microbes. The bioavailable metal fractions of HMs (Fe, Ni, Cd, Cu, Pb, and Cr) decreased by 61-83%. The correlation was performed for 0 and 90 days for metal microbial interactions r (0 days), [BSR vs Fe, Cd, Cu, Ni = -0.99, -0.82, -0.43, -0.99] and r (90 days), [FDA vs Fe, Cu, Ni = -0.97, -0.47, -0.95]. Overall, the results indicated that T1(1:1 SW + CD) provided more favorable conditions for the development of microbes and Eisenia fetida. This research presents a new perspective to the world community on the transformation of harmful steel waste slag into advantageous biological resources by introducing a novel method of employing Eisenia fetida to remediate hazardous steel waste slag.

Plastic and terrestrial organic matter degradation by the humic lake microbiome continues throughout the seasons

Boreal freshwaters go through four seasons, however, studies about the decomposition of terrestrial and plastic compounds often focus only on summer. We compared microbial decomposition of 13C-polyethylene, 13C-polystyrene, and 13C-plant litter (Typha latifolia) by determining the biochemical fate of the substrate carbon and identified the microbial decomposer taxa in humic lake waters in four seasons. For the first time, the annual decomposition rate including separated seasonal variation was calculated for microplastics and plant litter in the freshwater system. Polyethylene decomposition was not detected, whereas polystyrene and plant litter were degraded in all seasons. In winter, decomposition rates of polystyrene and plant litter were fivefold and fourfold slower than in summer, respectively. Carbon from each substrate was mainly respired in all seasons. Plant litter was utilized efficiently by various microbial groups, whereas polystyrene decomposition was limited to Alpha- and Gammaproteobacteria. The decomposition was not restricted only to the growth season, highlighting that the decomposition of both labile organic matter and extremely recalcitrant microplastics continues throughout the seasons.

Male, female, and mixed-sex poplar plantations support divergent soil microbial communities

Males and females of dioecious plants have sex-specific adaptations to diverse habitats. The effects of inter- and intrasexual interactions in poplar plantations on composition, structure, and function of soil microbiota have not been explored in degraded areas. We conducted a series of greenhouse and field experiments to investigate how belowground competition, soil microbial communities, and seasonal variation nitrogen content differ among female, male, and mixed-sex Populus cathayana plantations. In the greenhouse experiment, female neighbors suppressed the growth of males under optimal nitrogen conditions. However, male neighbors enhanced stable isotope ratio of nitrogen (δ15 N) of females under intersexual competition. In the field, the root length density, root area density, and biomass of fine roots were lower in female plantations than in male or mixed-sex plantations. Bacterial networks of female, male, and mixed-sex plantations were characterized by different composition of hub nodes, including connectors, modules, and network hubs. The sex composition of plantations altered bacterial and fungal community structures according to Bray-Curtis distances, with 44% and 65% of variance explained by the root biomass, respectively. The total soil nitrogen content of mixed-sex plantation was higher than that in female plantation in spring and summer. The mixed-sex plantation also had a higher β-1,4-N-acetyl-glucosaminidase activity in summer and a higher nitrification rate in autumn than the other two plantations. The seasonal soil N content, nitrification rate, and root distribution traits demonstrated spatiotemporal niche separation in the mixed-sex plantation. We argue that a strong female-female competition and limited nitrogen content could strongly impede plant growth and reduce the resistance of monosex plantations to climate change and the mixed-sex plantations constitutes a promising way to restore degraded land.

Warming influences carbon and nitrogen assimilation between a widespread Ericaceous shrub and root-associated fungi

High-latitude ecosystems are warming faster than other biomes and are often dominated by a ground layer of Ericaceous shrubs, which can respond positively to warming. The carbon-for-nitrogen (C-for-N) exchange between Ericaceous shrubs and root-associated fungi may underlie shrub responses to warming, but has been understudied. In a glasshouse setting, we examined the effects of warming on the C-for-N exchange between the Ericaceous shrub Empetrum nigrum ssp. hermaphroditum and its root-associated fungi. We applied different 13 C and 15 N isotope labels, including a simple organic N form (glycine) and a complex organic N form (moss litter) and quantified their assimilation into soil, plant biomass, and root fungal biomass pools. We found that warming lowered the amount of 13 C partitioned to root-associated fungi per unit of glycine 15 N assimilated by E. nigrum, but only in the short term. By contrast, warming increased the amount of 13 C partitioned to root-associated fungi per unit of moss 15 N assimilated by E. nigrum. Our study suggests that climate warming affects the short-term exchange of C and N between a widespread Ericaceous shrub and root-associated fungi. Furthermore, while most isotope tracing studies use labile N sources, we demonstrate that a ubiquitous recalcitrant N source may produce contrasting results.

Nitrogen addition accelerates litter decomposition and arsenic release of Pteris vittata in arsenic-contaminated soil from mine

The arsenic (As) release from litter decomposition of As-hyperaccumulator (Pteris vittata L.) in mine areas poses an ecological risk for metal dispersion into the soil. However, the effect of atmospheric nitrogen (N) deposition on the litter decomposition of As-hyperaccumulator in the tailing mine area remains poorly understood. In this study, we conducted a microcosm experiment to investigate the As release during the decomposition of P. vittata litter under four gradients of N addition (0, 5, 10, and 20 mg N g-1). The N10 treatment (10 mg N g-1) enhanced As release from P. vittata litter by 1.2-2.6 folds compared to control. Furthermore, Streptomyces, Pantoea, and Curtobacterium were found to primarily affect the As release during the litter decomposition process. Additionally, N addition decreased the soil pH, subsequently increased the microbial biomass, as well as hydrolase activities (NAG) which regulated N release. Thereby, N addition increased the As release from P. vittata litter and then transferred to the soil. Moreover, this process caused a transformation of non-labile As fractions into labile forms, resulting in an increase of available As concentration by 13.02-20.16% within the soil after a 90-day incubation period. Our findings provide valuable insights into assessing the ecological risk associated with As release from the decomposition of P. vittata litter towards the soil, particularly under elevated atmospheric N deposition.

Nitrogen deposition raises temperature sensitivity of soil organic matter decomposition in subtropical forest

Subtropical ecosystems are strongly affected by nitrogen (N) deposition, impacting soil organic matter (SOM) availability and stocks. Here we aimed to reveal the effects of N deposition on i) the structure and functioning of microbial communities and ii) the temperature sensitivity (Q10) of SOM decomposition. Phosphorus (P) limited evergreen forest in Guangdong Province, southeastern China, was selected, and N deposition (factor level: N (100 kg N ha-1 y-1 (NH4NO3)) and control (water), arranged into randomized complete block design (n = 3)) was performed during 2.5 y. After that soils from 0 to 20 cm were collected, analyzed for the set of parameters and incubated at 15, and 25, and 35 °C for 112 days. N deposition increased the microbial biomass N and the content of fungal and Gram-positive bacterial biomarkers; activities of beta-glucosidase (BG) and acid phosphatase (ACP) also increased showing the intensification of SOM decomposition. The Q10 of SOM decomposition under N deposition was 1.66 and increased by 1.4 times than under control. Xylosidase (BX), BG, and ACP activities increased with temperature under N but decreased with the incubation duration, indicating either low production and/or decomposition of enzymes. Activities of polyphenol-(PPO) and peroxidases (POD) were higher under N than in the control soil and were constant during the incubation showing the intensification of recalcitrant SOM decomposition. At the early incubation stage (10 days), the increase of Q10 of CO2 efflux was explained by the activities of BX, BQ, ACP, and POD and the quality of the available dissolved organic matter pool. At the later incubation stages (112 days), the drop of Q10 of CO2 efflux was due to the depletion of the labile organic substances and the shift of microbial community structure to K-strategists. Thus, N deposition decoupled the effects of extracellular enzyme activities from microbial community structure on Q10 of SOM decomposition in the subtropical forest soil.

Production of structurally diverse sphingolipids by anaerobic marine bacteria in the euxinic Black Sea water column

Microbial lipids, used as taxonomic markers and physiological indicators, have mainly been studied through cultivation. However, this approach is limited due to the scarcity of cultures of environmental microbes, thereby restricting insights into the diversity of lipids and their ecological roles. Addressing this limitation, here we apply metalipidomics combined with metagenomics in the Black Sea, classifying and tentatively identifying 1623 lipid-like species across 18 lipid classes. We discovered over 200 novel, abundant, and structurally diverse sphingolipids in euxinic waters, including unique 1-deoxysphingolipids with long-chain fatty acids and sulfur-containing groups. Sphingolipids were thought to be rare in bacteria and their molecular and ecological functions in bacterial membranes remain elusive. However, genomic analysis focused on sphingolipid biosynthesis genes revealed that members of 38 bacterial phyla in the Black Sea can synthesize sphingolipids, representing a 4-fold increase from previously known capabilities and accounting for up to 25% of the microbial community. These sphingolipids appear to be involved in oxidative stress response, cell wall remodeling, and are associated with the metabolism of nitrogen-containing molecules. Our findings underscore the effectiveness of multi-omics approaches in exploring microbial chemical ecology.

Subarctic winter warming promotes soil microbial resilience to freeze-thaw cycles and enhances the microbial carbon use efficiency

Climate change is predicted to cause milder winters and thus exacerbate soil freeze-thaw perturbations in the subarctic, recasting the environmental challenges that soil microorganisms need to endure. Historical exposure to environmental stressors can facilitate the microbial resilience to new cycles of that same stress. However, whether and how such microbial memory or stress legacy can modulate microbial responses to cycles of frost remains untested. Here, we conducted an in situ field experiment in a subarctic birch forest, where winter warming resulted in a substantial increase in the number and intensity of freeze-thaw events. After one season of winter warming, which raised mean surface and soil (-8 cm) temperatures by 2.9 and 1.4°C, respectively, we investigated whether the in situ warming-induced increase in frost cycles improved soil microbial resilience to an experimental freeze-thaw perturbation. We found that the resilience of microbial growth was enhanced in the winter warmed soil, which was associated with community differences across treatments. We also found that winter warming enhanced the resilience of bacteria more than fungi. In contrast, the respiration response to freeze-thaw was not affected by a legacy of winter warming. This translated into an enhanced microbial carbon-use efficiency in the winter warming treatments, which could promote the stabilization of soil carbon during such perturbations. Together, these findings highlight the importance of climate history in shaping current and future dynamics of soil microbial functioning to perturbations associated with climate change, with important implications for understanding the potential consequences on microbial-mediated biogeochemical cycles.

Plant Nutrition-New Methods Based on the Lessons of History: A Review

As with new technologies, plant nutrition has taken a big step forward in the last two decades. The main objective of this review is to briefly summarise the main pathways in modern plant nutrition and attract potential researchers and publishers to this area. First, this review highlights the importance of long-term field experiments, which provide us with valuable information about the effects of different applied strategies. The second part is dedicated to the new analytical technologies (tomography, spectrometry, and chromatography), intensively studied environments (rhizosphere, soil microbial communities, and enzymatic activity), nutrient relationship indexes, and the general importance of proper data evaluation. The third section is dedicated to the strategies of plant nutrition, i.e., (i) plant breeding, (ii) precision farming, (iii) fertiliser placement, (iv) biostimulants, (v) waste materials as a source of nutrients, and (vi) nanotechnologies. Finally, the increasing environmental risks related to plant nutrition, including biotic and abiotic stress, mainly the threat of soil salinity, are mentioned. In the 21st century, fertiliser application trends should be shifted to local application, precise farming, and nanotechnology; amended with ecofriendly organic fertilisers to ensure sustainable agricultural practices; and supported by new, highly effective crop varieties. To optimise agriculture, only the combination of the mentioned modern strategies supported by a proper analysis based on long-term observations seems to be a suitable pathway.

Spatiotemporal variation of microbial communities in surficial sediments of Cochin estuary, southwest coast of India

Microorganisms play a major role in the degradation of organic matter in sediments. However, the spatiotemporal variation and factors affecting these communities are not clearly understood. At the same time, conventional hydrographic and geochemical parameters do not offer an accurate assessment of transitional ecosystems. PLFA biomarkers which are specific to different taxonomic groups of microorganisms are able to provide a detailed assessment of the community composition in an environment and reflect a more direct assessment of the biological health of transitional ecosystems. We, therefore, conducted a comparison of PLFA biomarkers at four stations (Barmouth, B; Vaduthala, V; Munambam, M; and Arookutty, A) during three seasons (pre-monsoon, PRE; monsoon, MON; and post-monsoon, POST) in the Cochin estuary (CE). Each of the stations represented either a reference point (B), high pollution (V), high salinity (M), or low pollution (A). The communities determined using PLFA profiles could be categorized into six major groups with each group capable of reflecting the state of the ecosystem which correlated with the conventional parameters. The six groups were: G + ve Bacillota (formerly Firmicutes) and G-ve anaerobes (G-I), G-ve aerobic prokaryotes (G-II), ectomycorrhizal fungi (G-III), arbuscular mycorrhizae (G-IV), type-I methanotrophs (G-V), and microeukaryotes (G-VI). The prokaryotes were predominant in sediments amounting to over 78% of the total PLFAs detected, followed by the microeukaryotes. The freshwater-influenced stations were partially anaerobic in nature during PRE and MON and were mainly affected by both marine and terrestrial organic matter inputs, at times prominent in sewage matter. During POST season, CE behaves uniformly, especially in station M. Salinity and DO of BW and texture and organic matter of the sediment were the driving forces for microbial community structure. The reduced presence of cyclopropane fatty acids suggested that the CE was not under any stress during the study period. Our results using PLFA-based community profiling not only provide the fundamental information required to quickly access the impact of stress and other environmental inputs on the CE but also offer a more robust and realistic assessment of the nature of microbial communities in the ecosystem. A periodic and systemic assessment of PLFA profiles at these stations in CE throughout the year will enable the generation of enough metadata enabling a better understanding of this ecosystem and its efficient management in the long term.

Effects of flow velocity on biofilm composition and microbial molecular ecological network in reclaimed water distribution systems

The existence of biofilm on the reclaimed water pipeline seriously affects the safety of water distribution. And the flow regimes in the pipeline play a crucial role in the growth of biofilms. In this study, the biofilm composition, surface topography and bacterial community were detected under eight levels of flow velocity in the range of 0.10-1.40 m s-1. The results showed that the dry weight, the concentration of extracellular protein and extracellular polysaccharide in the biofilm reached a dynamic stable period after 640 h. The biofilm composition and surface topography of biofilm were significantly different under the different flow regimes (laminar flow belongs to [0.10, 0.19] m s-1, and turbulent flow belongs to [0.29, 1.40] m s-1). As the flow velocity range increases, the concentration of each component in the biofilm and the parameters of biofilm surface topography increased and then decreased. The flow velocity could be a strong environmental stimulus resulting in the succession of bacterial community in biofilm. As the flow velocity increased from 0.10 m s-1 to 1.40 m s-1, at the phylum level, the average relative abundance of Firmicutes mainly showed a trend of first increasing and then decreasing with the highest abundance value of 71.57% at 0.49 m s-1. The flow velocity increased from 0.10 m s-1 to 0.49 m s-1, a significant increase in microbial diversity could be detected. The increase in flow velocity promoted the proliferation of microorganisms, and the interaction between different microbial components was enhanced. At 0.49 m s-1, the function of the biofilm is complex, and the ability to resist environmental stress is the strongest. This study can effectively improve the cognition depth of biofilms under the influence of flow velocity in the reclaimed water distribution systems, and provide an important theoretical support for the safe distribution of reclaimed water.

Microbial degradation and assimilation of veratric acid in oxic and anoxic groundwaters

Microbial communities are key players in groundwater ecosystems. In this dark environment, heterotrophic microbes rely on biomass produced by the activity of lithoautotrophs or on the degradation of organic matter seeping from the surface. Most studies on bacterial diversity in groundwater habitats are based on 16S gene sequencing and full genome reconstructions showing potential metabolic pathways used in these habitats. However, molecular-based studies do not allow for the assessment of population dynamics over time or the assimilation of specific compounds and their biochemical transformation by microbial communities. Therefore, in this study, we combined DNA-, phospholipid fatty acid-, and metabolomic-stable isotope probing to target and identify heterotrophic bacteria in the groundwater setting of the Hainich Critical Zone Exploratory (CZE), focusing on 2 aquifers with different physico-chemical conditions (oxic and anoxic). We incubated groundwater from 4 different wells using either 13C-labeled veratric acid (a lignin-derived compound) (single labeling) or a combination of 13CO2 and D-labeled veratric acid (dual labeling). Our results show that heterotrophic activities dominate all groundwater sites. We identified bacteria with the potential to break down veratric acid (Sphingobium or Microbacterium). We observed differences in heterotrophic activities between the oxic and anoxic aquifers, indicating local adaptations of bacterial populations. The dual labeling experiments suggested that the serine pathway is an important carbon assimilation pathway and that organic matter was an important source of hydrogen in the newly produced lipids. These experiments also yielded different labeled taxa compared to the single labeling experiments, showing that there exists a complex interaction network in the groundwater habitats.

Influence of solids and hydraulic retention times on microbial diversity and removal of estrogens and nonylphenols in a pilot-scale activated sludge plant

The removal of EDCs in activated sludge processes can be enhanced by increasing solid and hydraulic retention times (SRT and HRT); it has been suggested that the improvement in removal is due to changes in microbial community structure (MCS). Though the influence of SRT and HRT on chemical removal and MCS has been studied in isolation, their synergistic impact on MCS and the removal of estrogens and nonylphenols in activated sludge remains unknown. Hence, we investigated how both parameters influence MCS in activated sludge processes and their ulterior effect on EDC removal. In our study, an activated sludge pilot-plant was fed with domestic sewage fortified with 100 and 1000 ng/L nonylphenols or 2 and 15 ng/L estrogens and operated at 3, 10 and 27 d SRT (constant HRT) and at 8, 16 and 24 h HRT (constant SRT). The MCS was assessed by phospholipid fatty acids (PLFA) analysis, and the archaeal and bacterial diversities were determined by 16S rRNA analysis. From the PLFA, the microbial abundance ranked as follows: Gram-negative > fungi > Gram-positive > actinomycetes whilst 16S rRNA analysis revealed Proteobacteria > Bacteroidetes > Others. Both PLFA and 16S rRNA analysis detected changes in MCS as SRT and HRT were increased. An SRT increment from 3 to 10 d resulted in higher estrone (E1) removal from 19 to 93% and nonylphenol-4-exthoxylate (NP4EO) from 44 to 73%. These findings demonstrate that EDC-removal in activated sludge plants can be optimised where longer SRT (>10 d) and HRT (>8 h) are suitable. We have also demonstrated that PLFA can be used for routine monitoring of changes in MCS in activated sludge plants.

Asthma-protective agents in dust from traditional farm environments

BACKGROUND

Growing up on traditional European or US Amish dairy farms in close contact with cows and hay protects children against asthma, and airway administration of extracts from dust collected from cowsheds of those farms prevents allergic asthma in mice.

OBJECTIVES

This study sought to begin identifying farm-derived asthma-protective agents.

METHODS

Our work unfolded along 2 unbiased and independent but complementary discovery paths. Dust extracts (DEs) from protective and nonprotective farms (European and Amish cowsheds vs European sheep sheds) were analyzed by comparative nuclear magnetic resonance profiling and differential proteomics. Bioactivity-guided size fractionation focused on protective Amish cowshed DEs. Multiple in vitro and in vivo functional assays were used in both paths. Some of the proteins thus identified were characterized by in-solution and in-gel sodium dodecyl sulfate-polyacrylamide gel electrophoresis enzymatic digestion/peptide mapping followed by liquid chromatography/mass spectrometry. The cargo carried by these proteins was analyzed by untargeted liquid chromatography-high-resolution mass spectrometry.

RESULTS

Twelve carrier proteins of animal and plant origin, including the bovine lipocalins Bos d 2 and odorant binding protein, were enriched in DEs from protective European cowsheds. A potent asthma-protective fraction of Amish cowshed DEs (≈0.5% of the total carbon content of unfractionated extracts) contained 7 animal and plant proteins, including Bos d 2 and odorant binding protein loaded with fatty acid metabolites from plants, bacteria, and fungi.

CONCLUSIONS

Animals and plants from traditional farms produce proteins that transport hydrophobic microbial and plant metabolites. When delivered to mucosal surfaces, these agents might regulate airway responses.

Responses of soil microbial communities and enzyme activities under nitrogen addition in fluvo-aquic and black soil of North China

This research investigates the impact of long-term nitrogen (N) addition on fluvo-aquic and black soils in north China, with a focus on soil microbial communities and enzyme activities. In each site, there were three N fertilization treatments, i.e., control, moderate-N, and high-N. Phospholipid Fatty Acid Analysis was employed to analyze the microbial community composition, and enzyme activities related to N, carbon (C), and phosphorus (P) cycling were assessed. The results showed that increasing N fertilization levels led to higher soil organic carbon (SOC) and total N (TN) concentrations, indicating enhanced nutrient availability. N fertilization reduced soil pH across both soils, with a more pronounced acidification effect observed in the black soil. Across both soils, N addition increased maize yield, but the higher crop yield was attained in moderate-N rate compared with high-N rate. Microbial community composition analysis revealed that N fertilization induced shifts in the relative abundances of specific microbial groups. The black soil exhibited pronounced shifts in the microbial groups compared to the fluvo-aquic soil, i.e., decreased fungal abundance and fungi: bacteria ratio in response to N input. In addition, the application of N fertilizer led to an elevated ratio of gram-positive to gram-negative (GP:GN) bacteria, but this effect was observed only in black soil. N fertilization had an impact on the enzyme activities related to C, N, and P cycling in both soil types, but black soil showed more pronounced changes in enzyme activities. Permutational multivariate analysis of variance indicated that soil types rather than N fertilization mediated the response of the soil microbial community and enzyme activities. Partial least square path modeling demonstrated that soil pH was the only key driver impacting soil microbial groups and enzyme activities in both soils. In conclusion, our findings highlighted that N fertilization exerted more pronounced impacts on soil biochemical properties, microbial community composition, and enzyme activities in black soil furthermore, moderate N rate resulted in higher crop productivity over high N rate.

A carbonate corrosion experiment at a marine methane seep: The role of aerobic methanotrophic bacteria

Methane seeps are typified by the formation of authigenic carbonates, many of which exhibit corrosion surfaces and secondary porosity believed to be caused by microbial carbonate dissolution. Aerobic methane oxidation and sulfur oxidation are two processes capable of inducing carbonate corrosion at methane seeps. Although the potential of aerobic methanotrophy to dissolve carbonate was confirmed in laboratory experiments, this process has not been studied in the environment to date. Here, we report on a carbonate corrosion experiment carried out in the REGAB Pockmark, Gabon-Congo-Angola passive margin, in which marble cubes were deployed for 2.5 years at two sites (CAB-B and CAB-C) with apparent active methane seepage and one site (CAB-D) without methane seepage. Marble cubes exposed to active seepage (experiment CAB-C) were found to be affected by a new type of microbioerosion. Based on 16S rRNA gene analysis, the biofilms adhering to the bioeroded marble mostly consisted of aerobic methanotrophic bacteria, predominantly belonging to the uncultured Hyd24-01 clade. The presence of abundant ¹³ C-depleted lipid biomarkers including fatty acids (n-C_16:1ω8c , n-C_18:1ω8c , n-C_16:1ω5t ), various 4-mono- and 4,4-dimethyl sterols, and diplopterol agrees with the dominance of aerobic methanotrophs in the CAB-C biofilms. Among the lipids of aerobic methanotrophs, the uncommon 4α-methylcholest-8(14)-en-3β,25-diol is interpreted to be a specific biomarker for the Hyd24-01 clade. The combination of textural, genetic, and organic geochemical evidence suggests that aerobic methanotrophs are the main drivers of carbonate dissolution observed in the CAB-C experiment at the REGAB pockmark.

Legume Overseeding and P Fertilization Increases Microbial Activity and Decreases the Relative Abundance of AM Fungi in Pampas Natural Pastures

Natural grasslands provide a valuable resource for livestock grazing. In many parts of South America, legume overseeding and P fertilization are commonly used to enhance primary productivity. The effect of this practice on the plant community is well established. However, how this management regime affects the soil microbiome is less known. Here, to contribute to filling this knowledge gap, we analyzed the effect of Lotus subbiflorus overseeding, together with P fertilization, on soil microbial community diversity and activity in the Uruguayan Pampa region. The results showed that plant communities in the natural grassland paddocks significantly differed from those of the managed paddocks. In contrast, neither microbial biomass and respiration nor microbial diversity was significantly affected by management, although the structure of the bacterial and fungal communities were correlated with those of the plant communities. AM Fungi relative abundance, as well as several enzyme activities, were significantly affected by management. This could have consequences for the C, N, and P content of SOM in these soils, which in turn might affect SOM degradation.

The two sides of resistance-resilience relationship in both aboveground and belowground communities in the Eurasian steppe

The ongoing nitrogen (N) deposition has led to profound changes in aboveground and belowground ecosystems. However, the stability of plant and soil microbial community toward N addition in terms of resistance and resilience is less understood. We established a long-running field trial (2008-2018) in a series of N applications in combination with a mowing and fencing (unmown) treatment in a semiarid steppe. We assessed the resistance via ongoing N treatment of one subplot and the resilience via discontinuing N treatment in another to promote natural recovery since 2014. Plant resistance was negatively correlated with N application rate, while microbial resistance was independent of N rate. Mowing significantly reduced plant resistance and resilience, reduced soil microbial resistance but improved its resilience. Generally, plants are more resilient but less resistant to N than soil microbes. The two sides of resistance-resilience relationship were revealed: trade-offs exist between resistance and resilience for both plants and microbes at the community level; and trade-offs between resistance and resilience cannot be scaled down to species/group level. This study provided an important theoretical basis for the recovery and conservation of semiarid steppe and new insight into resistance-resilience relationship.

Characteristics of organic pollutants and their effects on the microbial composition and activity in the industrial soils of Pearl River Delta, China

To investigate the interaction between organic pollutants and soil microorganisms, industrial soils were collected from Pearl River Delta region of China for determining semi-volatile organic pollutants, the community structure and activity of microorganisms. The results showed that polycyclic aromatic hydrocarbons (PAHs) (63.3-4956 μg kg^-1) and phthalate esters (PAEs) (272-65,837 μg kg^-1) were main organic pollutants in the research area soils. Chemical manufacturing industry and plastics manufacturing industry contributed greatly to PAH pollution and PAE pollution, respectively. Organic pollutants changed the biomass of microorganisms. In most industrial soils, the biomass of actinomycetes was the highest in the industrial soils, followed by G^- bacteria, G⁺ bacteria and fungi. The exception was that the biomass of fungi in the soil near chemical manufacturing industry was greater than that of G⁺ bacteria. The soil microbial biomass (including soil microbial biomass carbon, soil microbial biomass nitrogen, the biomass of actinomycetes, bacteria, and fungi) and soil enzyme activities (sucrase and urease) positively correlated with the organic pollutant residues, and the microbial species diversity and microbial species abundance decreased with organic pollutant residues increasing. Based on the correlation analysis, the urease activity, actinomycetes biomass, and fungi biomass were appropriate biological indicators for evaluating the stress of organic pollutants. Our research provides a new perspective for understanding the soil biological response in industrial soils.

High carbon emissions from thermokarst lakes and their determinants in the Tibet Plateau

Thermokarst lakes are potentially important sources of methane (CH₄ ) and carbon dioxide (CO₂ ). However, considerable uncertainty exists regarding carbon emissions from thermokarst lakes owing to a limited understanding of their patterns and motivators. In this study, we measured CH₄ and CO₂ diffusive fluxes in 163 thermokarst lakes in the Qinghai-Tibet Plateau (QTP) over 3 years from May to October. The median carbon emissions from the QTP thermokarst lakes were 1440 mg CO₂ m^-2 day^-1 and 60 mg CH₄ m^-2 day^-1 , respectively. The diffusive rates of CO₂ and CH₄ are related to the catchment land cover type. Sediment microbial abundance and hydrochemistry explain 51.9% and 38.3% of the total variance in CH₄ diffusive emissions, respectively, while CO₂ emissions show no significant relationship with environmental factors. When upscaling carbon emissions from the QTP thermokarst lakes, the annual average CH₄ release per lake area is equal to that of the pan-Arctic region. Our findings highlight the importance of incorporating in situ observation data with different emission pathways for different land cover types in predicting carbon emissions from thermokarst lakes in the future.

Ex situ bioremediation of diesel fuel-contaminated soil in two different climates

The petroleum industry is often faced with accidental spills and discharges that pollute valuable natural resources such as soil. The purpose of this study was to assess bioremediation potential of an on-site landfarming unit (LU), a highly economical solution that complies with the zero-waste policy, for bioremediation of the contaminated soil after an actual diesel fuel leakage in a fuel depot. The first aim was to evaluate the effects of different climates on hydrocarbon bioremediation. For this reason, a part of the contaminated soil was moved from the initial location with a sub-Mediterranean climate to an LU at another location with a temperate continental climate. Our results demonstrated that remediation in sub-Mediterranean climate is less effective than the remediation in a temperate continental climate. The second aim of this study was to evaluate the effect of different plant species on the microbial population during bioremediation. For that purpose, 365-day monitoring of phospholipid fatty acids (PLFA) was performed. Our results support the hypothesis that plant-assisted bioremediation can diminish toxic effects of diesel-polluted soil and that the changes in plant species during bioremediation cause changes in the microbial population.

Hydrogen stable isotope probing of lipids demonstrates slow rates of microbial growth in soil

The rate at which microorganisms grow and reproduce is fundamental to our understanding of microbial physiology and ecology. While soil microbiologists routinely quantify soil microbial biomass levels and the growth rates of individual taxa in culture, there is a limited understanding of how quickly microbes actually grow in soil. For this work, we posed the simple question: what are the growth rates of soil microorganisms? In this study, we measure these rates in three distinct soil environments using hydrogen-stable isotope probing of lipids with 2H-enriched water. This technique provides a taxa-agnostic quantification of in situ microbial growth from the degree of 2H enrichment of intact polar lipid compounds ascribed to bacteria and fungi. We find that growth rates in soil are quite slow and correspond to average generation times of 14 to 45 d but are also highly variable at the compound-specific level (4 to 402 d), suggesting differential growth rates among community subsets. We observe that low-biomass microbial communities exhibit more rapid growth rates than high-biomass communities, highlighting that biomass quantity alone does not predict microbial productivity in soil. Furthermore, within a given soil, the rates at which specific lipids are being synthesized do not relate to their quantity, suggesting a general decoupling of microbial abundance and growth in soil microbiomes. More generally, we demonstrate the utility of lipid-stable isotope probing for measuring microbial growth rates in soil and highlight the importance of measuring growth rates to complement more standard analyses of soil microbial communities.

Trophic ecology of three marine polychaete species: Evidence from laboratory experiments using stable isotope (15N, 13C), fatty acid (NLFA) analyses, and C and N stoichiometry

Marine polychaetes are a highly diverse taxon with a large variety of different feeding modes. A proper identification of the different diets of polychaete species and their trophic position in the food web is crucial for understanding their interactions in marine ecosystems as well as marine community dynamics. Since gut content analyses and feeding experiments are difficult to conduct in marine habitats, other methods using biochemical tracers may contribute to a better understanding of the trophic ecology of marine polychaetes. Here, we conducted laboratory experiments and used a combination of stable isotope (¹³C, ¹⁵N) and neutral lipid fatty acid (NLFA) analyses, as well as C and N stoichiometry to determine the feeding habits of widely distributed marine polychaete species, such as Eurythoe complanata, Platynereis massiliensis, and Syllis malaquini. Additionally, the impact of starvation on the stable isotope signatures was analyzed. Our data show that the trophic ecology of the three species differs from each other. Stable isotope and fatty acid analyses indicate that (a) E. complanata is mainly feeding on algae, cyanobacteria and to a lesser extent on fungi, that (b) S. malaquini is mainly feeding on algae and bacteria and that (c) P. massiliensis is mainly feeding on algae, especially diatoms. An analysis of the C:N ratio of the respective annelid species and their potential food sources corroborated these results. The combination of stable isotope signatures, fatty acid markers and stoichiometry of carbon and nitrogen is a useful tool to identify the diet and trophic position of marine polychaete species and provides more results about their feeding habits and their position in marine food webs.

Decoding the PLFA profiling of microbial community structure in soils contaminated with municipal solid wastes

This study aimed to assess the influence of municipal solid waste (MSW) disposal on soil microbial communities. Soil samples from 20 different locations of an MSW dumping site contaminated with toxic heavy metals (HMs) and a native forest (as control) were collected for phospholipid fatty acid (PLFA) profiling to predict microbial community responses towards unsegregated disposal of MSW. PLFA biomarkers specific to arbuscular mycorrhizal fungi (AMF), Gram-negative and Gram-positive bacteria, fungi, eukaryotes, actinomycetes, anaerobes, and microbial stress markers-fungi: bacteria (F/B) ratio, Gram-positive/Gram-negative (GP/GN) ratio, Gram-negative stress (GNStr) ratio and predator/prey ratio along with AMF spore density and the total HM content (Cu, Cr, Cd, Mn, Zn, and Ni) were assessed. The results showed that all of the PLFA microbial biomarkers and the F/B ratio were positively correlated, while HMs and microbial stress markers were negatively correlated. The significant correlation of AMF biomass with all microbial groups, the F/B ratio, and T. PLFA confirmed its significance as a key predictor of microbial biomass. With AMF and T. PLFA, Cd and Cr had a weak or negative connection. Among the toxic HMs, Zn and Cd had the greatest impact on microbial populations. Vegetation did not have any significant effect on soil microbial communities. This research will aid in the development of bioinoculants for the bioremediation of MSW-polluted sites and will improve our understanding of the soil microbial community's ability to resist, recover, and adapt to toxic waste contamination.

Leaching of phthalate acid esters from plastic mulch films and their degradation in response to UV irradiation and contrasting soil conditions

Phthalate acid esters (PAEs) are commonly used plastic additives, not chemically bound to the plastic that migrate into surrounding environments, posing a threat to environmental and human health. Dibutyl phthalate (DBP) and di(2-ethylhexyl) phthalate (DEHP) are two common PAEs found in agricultural soils, where degradation is attributed to microbial decomposition. Yet the impact of the plastic matrix on PAE degradation rates is poorly understood. Using ¹⁴C-labelled DBP and DEHP we show that migration from the plastic matrix into soil represents a key rate limiting step in their bioavailability and subsequent degradation. Incorporating PAEs into plastic film decreased their degradation in soil, DBP (DEHP) from 79% to 21% (9% to <1%), over four months when compared to direct application of PAEs. Mimicking surface soil conditions, we demonstrated that exposure to ultraviolet radiation accelerated PAE mineralisation twofold. Turnover of PAE was promoted by the addition of biosolids, while the presence of plants and other organic residues failed to promote degradation. We conclude that PAEs persist in soil for longer than previously thought due to physical trapping within the plastic matrix, suggesting PAEs released from plastics over very long time periods lead to increasing levels of contamination.

Effects of applying peanut shell and its biochar on the microbial activity and community structure of dryland red soil

Due to its soil formation process, dryland red soil has certain characteristics that are unfavorable for crop growth, including acidity, fineness, plate structures, and erosivity. The use of large amounts of fertilizer can decrease fertility and biodiversity and increase acidification, thereby seriously restricting the sustainable utilization of dryland red soil resources. Therefore, there is an urgent need for techniques that improve the crop quality and yield in dryland red soil areas. Returning crop waste to fields as fertilizer is a promising approach to sustainable agriculture. In the present study, the effects of applying peanut shell and an associated biochar product to dryland red soil were investigated, with a focus on soil microbial activity and community structure. Field experiments were conducted in Jiangxi Province, southern China, in 2020, in field plots of sweet potato crops. Seven treatments were set up according to the principle of equal carbon return to farmland: Control: (conventional fertilization); S1, S2, S3 (peanut shell application of 3000, 4500 and 6000 kg hm^-2, respectively); and BC1, BC2, BC3 (peanut shell biochar application of 1000, 1500 and 2000 kg hm^-2, respectively). The application of peanut shell and its biochar improved soil basal respiration, with the greatest increase relative to controls of 161.06% found in treatment S3 at the root harvest stage. The most obvious increase in microbial biomass carbon content due to biochar application was 206.50% in treatment BC2 at the root harvest stage. The application of peanut shell and its biochar increased the phospholipid fatty acid (PLFA) contents of total soil microorganisms and different microbial groups. The maximum increases in the PLFA contents of total soil microorganisms, gram-positive bacteria, and gram-negative bacteria occurred at the early root formation stage in treatment BC2, which were 112.16%, 102.52%, and 115.64%, respectively. Both peanut shell and biochar increased the PLFA contents of soil actinomycetes, arbuscular mycorrhizal fungi (AMF), and other fungi to certain extents. The soil actinomycetes PLFAs increased by 120.08% at the early root formation stage in BC2, while the AMF PLFAs increased by 79.44% at the seedling stage in S2. This study provides theoretical and practical guidance for the comprehensive utilization of peanut shell and the implementation of circular agriculture in dryland red soil regions. It also provides a scientific basis for improving the fertility of dryland red soil.

Decomposition rate and biochemical fate of carbon from natural polymers and microplastics in boreal lakes

Microbial mineralization of organic compounds is essential for carbon recycling in food webs. Microbes can decompose terrestrial recalcitrant and semi-recalcitrant polymers such as lignin and cellulose, which are precursors for humus formation. In addition to naturally occurring recalcitrant substrates, microplastics have been found in various aquatic environments. However, microbial utilization of lignin, hemicellulose, and microplastics as carbon sources in freshwaters and their biochemical fate and mineralization rate in freshwaters is poorly understood. To fill this knowledge gap, we investigated the biochemical fate and mineralization rates of several natural and synthetic polymer-derived carbon in clear and humic lake waters. We used stable isotope analysis to unravel the decomposition processes of different 13C-labeled substrates [polyethylene, polypropylene, polystyrene, lignin/hemicellulose, and leaves (Fagus sylvatica)]. We also used compound-specific isotope analysis and molecular biology to identify microbes associated with used substrates. Leaves and hemicellulose were rapidly decomposed compared to microplastics which were degraded slowly or below detection level. Furthermore, aromatic polystyrene was decomposed faster than aliphatic polyethylene and polypropylene. The major biochemical fate of decomposed substrate carbon was in microbial biomass. Bacteria were the main decomposers of all studied substrates, whereas fungal contribution was poor. Bacteria from the family Burkholderiaceae were identified as potential leaf and polystyrene decomposers, whereas polypropylene and polyethylene were not decomposed.

The influence of increased precipitation and nitrogen deposition on the litter decomposition and soil microbial community structure in a semiarid grassland

Litter decomposition is a major method in which nutrients are recycled, especially carbon and nitrogen elements, in terrestrial ecosystems. However, how the responses of litter quality and soil microbial communities to global changes alter litter decomposition remains unclear. A 4-year field manipulative experiment based on the litterbag method was conducted in a typical temperate semiarid grassland in China to explore how increased precipitation and nitrogen deposition affect decomposition processes via litter quality and soil microbial communities. Our results showed that water and nitrogen addition treatments could accelerate litter carbon release and promote mass loss through different pathways. Water addition had a direct positive effect on litter decomposition. However, nitrogen addition could indirectly promote litter decomposition by improving litter quality and increasing the bacterial and fungal ratios. The water addition treatment increased litter mass loss by 7.37 %, and the N addition treatments increased litter mass loss by 5.83 %-16.93 %. Moreover, water and nitrogen additions had antagonistic effects on litter decomposition. These findings revealed that litter quality and the soil bacterial to fungal ratio were the factors controlling litter decomposition. The changes in precipitation and nitrogen deposition will impact ecosystem carbon and nitrogen cycling by altering litter decomposition processes in semiarid grassland ecosystems under the context of climate change.

Agricultural soil physico-chemical parameters and microbial abundance and diversity under long-run farming practices: A greenhouse study

The growth of agriculture led to indiscriminate use of synthetic pesticides or fertilizers and unsustainable crop management farming practices which can aggravate harmful impacts on the microbial population and physical and chemical characteristics of soil ecosystem. Based on this fact, the present study was planned to evaluate the effect of long run farming practices on different soil physico-chemical parameters and soil microbial abundance and diversity within different soil depth (0–20 cm and 20–40 cm) at Quzhou Experimental Station of China Agricultural University, Hebei, China during October and December, 2016. The effect of farming practices on soil microbial abundance and diversity was studied by phospho-lipid fatty acid (PLFA) and DNA high-throughput sequencing methods. The findings revealed that soil is neutral to slightly alkaline in nature with highest water content under organic farming (ORF) at 0–20 cm and least under conventional farming at 20–40 cm depth. It was found that the ORF significantly increased the contents of total organic carbon (TOC), total carbon (TC), ammonium nitrogen, available nitrogen (AN), total nitrogen (TN), total phosphorus (TP), and available phosphorus (AP) followed by low input and conventional farming modes in both October and December soil samples. The correlation analysis showed significantly (at p ≤ 0.05 and 0.01) strong positive relationship within different physical and chemical properties of the soil under study. ANOVA and MANOVA analysis indicated significant effect of interaction between soil depth and farming modes on soil parameters. PCA analysis showed the most significant correlation between most of the bacterial types (G + bacteria, G− bacteria, actinomycetes) and soil AP, total available nitrogen, TOC and soil WC. Pearson correlation analysis revealed a significant correlation between microbial phylum groups (Proteobacteria, Bacteroidetes, and Latescibacteria) and microbial class group (Alphaproteobacteria, Sphingobacteriia, Flavobacteriia) with most of the soil physicochemical properties.

The effect of Escherichia coli ŽP strain with a conjugation-based colicin E7 delivery on growth performance, hematological, biochemical, and histological parameters, gut microbiota, and nonspecific immunity of broilers

The Escherichia coli ŽP strain (ŽP) was constructed based on the known probiotic E. coli strain Nissle 1917. It was genetically modified to carry the colicin E7 synthesis gene encoding DNase on a conjugative plasmid and the colicin E7 immunity gene in the chromosome. The aim of this study was to evaluate the effects of the daily ŽP per oral administration (5 × 10⁸ or 5 × 10¹⁰ CFU per bird) on the growth performance, hematological, biochemical, histological parameters, gut microbiota, and nonspecific immunity of the 4-24 days old broilers. The ŽP administration increased the abundance of genera Bacillus, Butyrivibrio, and Clostridium and did not influence the weight gain of 4-16 days old broilers. The biochemical parameters were within normal ranges for poultry in experimental and control groups. The ŽP administration had no effect on the erythrocyte numbers, hemoglobin and immunoglobulin Y concentrations, but significantly increased the serum lysozyme concentration, leukocyte numbers, and reactive oxygen species production by phagocytes compared with the control group. It did not cause inflammatory changes in intestinal mucosa, Peyer's patches, and spleen. Thus, the ŽP had no detrimental effects on broiler health and could be an efficient probiotic for the broiler colibacillosis prophylaxis.

Stable isotopes (δ13C, δ15N) and biomarkers as indicators of the hydrological regime of fens in a European east-west transect

Peatland degradation is tightly connected to hydrological changes and microbial metabolism. To better understand these metabolism processes, more information is needed on how microbial communities and substrate cycling are affected by changing hydrological regimes. These activities should be imprinted in stable isotope bulk values (δ ¹⁵N, δ ¹³C) due to specific isotopic fractionation by different microbial communities, their metabolic pathways and nutrient sources. We hypothesize that stable isotope values and microbial abundance are correlated and act as indicators of different hydrological regimes. We sampled an East-West transect across European fens in 14 areas and conducted a stable isotope (δ ¹³C, δ ¹⁵N) and membrane fatty acid (mFA) analysis. Within each area an undrained, drained and rewetted site was selected. Rewetted sites were separated based on when rewetting occurred. We found differences in the upper layers of all sites in microbial-derived mFAs and stable isotope values corresponding to hydrological regimes. The highest and lowest quantities of microbial-derived mFAs were measured in undrained and drained sites, respectively. Fungal-derived mFAs were especially lower in drained sites. Simultaneously, δ¹⁵N stable isotope values were highest in drained sites. In addition, stable isotope values and microbial-derived mFAs showed distinct depth trends. In undrained sites stable isotopes values slightly increased with depth. In drained sites, δ¹⁵N values decreased downwards, whereas δ¹³C values increased. Overall microbial-derived mFAs decreased with depth. These patterns presumably result from anoxic conditions and high peat recalcitrance in the deeper layers. In sites with short time of rewetting, the microbial-derived mFAs and stable isotope values were similar to values of drained sites, while with increasing rewetting time values shifted to those of undrained sites. We conclude that biomarkers indicate that stable isotope values reflect specific microbial metabolic processes, which differ with hydrological regimes, and thus could indicate both drainage and rewetting in fens.

The Effect of Heavy Metals on Microbial Communities in Industrial Soil in the Area of Piekary Śląskie and Bukowno (Poland)

The aim of this study was to determine the activity and structure of microbial communities in soils contaminated with heavy metals (HMs). To achieve this goal, soil samples were taken from two contaminated sites (i.e., Piekary Śląskie and Bukowno) in Poland. A wide range of methods were applied, including: total and metal-tolerant culturable bacteria enumeration; microbial community structure analysis using the phospholipid fatty acid method (PLFA); denaturing gradient gel electrophoresis (PCR-DGGE); and metabolic activity using BIOLOG and EcoPlateTM. Our studies showed that HMs negatively affected microbial community structure and activity in polluted soils. Apart from the contamination with HMs, other soil parameters like soil pH and water also impacted microbial community structure and growth. Metal-tolerant bacterial strains were isolated, identified and tested for presence of genes encoding HM tolerance using the polymerase chain reaction (PCR) methodology. Contamination with HMs in the tested areas was found to lead to development of metallotolerant bacteria with multiple tolerances toward Zn, Ni, Cd and Cu. Different genes (e.g., czcA, cadA and nccA) encoding HM efflux pumps were detected within isolated bacteria. Culturable bacteria isolated belonged to Proteobacteria, Actinobacteria and Bacteroidetes genera. Among non-culturable bacteria in soil samples, a significant fraction of the total bacteria and phyla, such as Gemmatimonadetes and Acidobacteria, were found to be present in all studied soils. In addition, bacteria of the Chloroflexi genus was present in soil samples from Piekary Śląskie, while bacteria of the Firmicutes genus were found in soil samples from Bukowno.

Effects of mycorrhiza and hyphae on the response of soil microbial community to warming in eastern Tibetan Plateau

The effects of mycorrhiza and its external hyphae on the response of soil microbes to global warming remain unclear. This study investigates the role of mycorrhiza and its hyphae in regulating soil microbial community under warming by examining the microbial biomass and composition in the ingrowth cores of arbuscular mycorrhiza (AM) plant, Fargesia nitida, and ectomycorrhiza (ECM) plant, Picea asperata, with/without mycorrhiza/hyphae and experimental warming. The results showed that warming significantly increased the biomass of all soil microbes (by 19.89%-137.48%) and altered the microbial composition in both plant plots without mycorrhiza/hyphae. However, this effect was weakened in the presence of mycorrhiza or hyphae. In F. nitida plots, warming did not significantly affect biomass and composition of most soil microbial groups when mycorrhiza or hyphae were present. In P. asperata plots, warming significantly increased the total and ECM fungi (ECMF) biomass in the presence of hyphae (p < 0.05) and the total, Gn, and AM fungi (AMF) biomass in the presence of mycorrhiza (p < 0.05). Meanwhile, the response of enzyme activities to warming was also altered with mycorrhiza or hyphae. Additionally, soil microbial community composition was mainly influenced by soil available phosphorus (avaP), while enzyme activities depended on soil avaP, dissolved organic carbon (DOC), and nitrate concentrations. Our results indicate that mycorrhiza and its hyphae are essential in regulating the response of microbes to warming.

Nitrogen Fertilization Increases Soil Microbial Biomass and Alters Microbial Composition Especially Under Low Soil Water Availability

Soil microbial biomass and composition are affected by resource supply and water availability. However, the response of soil microbial communities to nitrogen fertilization under different water availability conditions is unclear. Therefore, this study conducted a 6-year pot experiment comprising five watering regimes (40%, 50%, 60%, 80%, and 100% of field capacity (FC)) and three nitrogen fertilization levels (NH₄NO₃ solution; 0 [N0], 20 [N1], and 40 [N2] g N m^-2 year^-1) to investigate soil microbial biomass, composition, and properties. The results indicated that soil microbial biomass and composition were more strongly affected by nitrogen fertilization compared with water regime. Nitrogen fertilization increased soil microbial biomass and altered soil microbial community composition, especially under low soil water availability. Soil microbial biomass was positively linearly associated with soil water regimes under N0, whereas it responded polynomially to soil water regimes under N1 and N2. The maximal soil microbial biomass was observed at FC80 for N1 and FC60 for N2. Furthermore, the biomass of soil microbial groups with high nitrogen and carbon acquisition ability as well as the enzyme activities of carbon and nitrogen cycling (β-1,4-glucosidase and β-1,4-N-acetyl-glucosaminidase, respectively) were stimulated by nitrogen fertilization. Soil microbial biomass was affected directly by nitrogen fertilization and indirectly by nitrogen and water regimes, via altering soil pH, dissolved inorganic nitrogen (NH₄⁺-N and NO₃^--N) concentration, and soil organic carbon concentration. This study provides new insights into the effect of interaction between soil nitrogen and water availabilities on soil microbial biomass, composition, and its underlying mechanism.

Evaluation of changes in the microbial community structure in the sediments of a constructed wetland over the years

This study presents the results of the long term (2007-2014) monitoring of the microbial community structure in the surface sediments of the H-02 constructed wetland system, which was built on the Savannah River Site in Aiken, SC, USA, to treat the waste water generated at the Tritium facility. Microbial community structure provides valuable information about the functioning of constructed wetlands and helps understand the biogeochemical cycling of nutrients and contaminants. Phospholipids fatty acid (PLFA) analysis and qPCR were used to identify major bacterial phyla in the sediments. The physiochemical properties of the sediments were also used to deduce potential effects on the microbial community structure over the years. Sulfate-reducing bacteria (SRB) were the most dominant bacterial groups, and their prevalence was progressively increasing throughout the years most likely on the account of methane producers. Concentrations of trace metals (copper and zinc) were negatively associated with methane producers and oxidizer while positively correlated with SRB. Overall, the H-02 wetland system was efficient in immobilizing copper and zinc through the anaerobic respiration of sulfate by SRB and minimizing methane emission through the progressive elimination of methane producers by SRB and Geobacter. The aim of this study was to monitor the changes in the microbial community structure in the surface sediments of a constructed wetland during the first 7 years of operation.

Patterns of microbial communities were shaped by bioavailable P along the elevation gradient of Shergyla Mountain, as determined by analysis of phospholipid fatty acids

The distribution pattern of the microbial community in mountains is an important component of biodiversity research. Many environmental factors vary significantly with elevation on a relatively small scale in subalpine and alpine environments. These factors may markedly affect microbial community composition and function. In this study, we analyzed phospholipid fatty acid (PLFA) profiles and phosphorus (P) fractions in soils from 9 sites along an elevation gradient (3500–4100 m above sea level (a.s.l.)) of the Shergyla Mountain, Tibet in China. Many biomarker PLFAs indicated that there were biogeochemical trends of the microbial distribution patterns of some soil microorganisms, which were most often increasing, U-shaped and unimodal trends along the elevation gradient. A redundancy analysis (RDA) and correlations indicated that P factors (e.g., Resin-Pi, NaHCO₃-Pi and NaHCO₃-Po) were more important in controlling the microbial PLFA distribution pattern than other factors (e.g., MAT, MAP, pH, TOC, TN and soil moisture) in this study area. Microorganisms are strongly associated with P fractions. Our results suggested that microbial communities were subjected to P stresses and that the distribution patterns of microbial communities were shaped by bioavailable P along the elevation gradient. Our work also hints that P geochemical processes drive the microbial diversity of the Shergyla Mountains.

Phosphorus addition decreases plant lignin but increases microbial necromass contribution to soil organic carbon in a subalpine forest

Increasing phosphorus (P) inputs induced by anthropogenic activities have increased P availability in soils considerably, with dramatic effects on carbon (C) cycling and storage. However, the underlying mechanisms via which P drives plant and microbial regulation of soil organic C (SOC) formation and stabilization remain unclear, hampering the accurate projection of soil C sequestration under future global change scenarios. Taking the advantage of an 8-year field experiment with increasing P addition levels in a subalpine forest on the eastern Tibetan Plateau, we explored plant C inputs, soil microbial communities, plant and microbial biomarkers, as well as SOC physical and chemical fractions. We found that continuous P addition reduced fine root biomass, but did not affect total SOC content. P addition decreased plant lignin contribution to SOC, primarily from declined vanillyl-type phenols, which was coincided with a reduction in methoxyl/N-alkyl C by 2.1%-5.5%. Despite a decline in lignin decomposition due to suppressed oxidase activity by P addition, the content of lignin-derived compounds decreased because of low C input from fine roots. In contrast, P addition increased microbial (mainly fungal) necromass and its contribution to SOC due to the slower necromass decomposition under reduced N-acquisition enzyme activity. The larger microbial necromass contribution to SOC corresponded with a 9.1%-12.4% increase in carbonyl C abundance. Moreover, P addition had no influence on the slow-cycing mineral-associated organic C pool, and SOC chemical stability indicated by aliphaticity and recalcitrance indices. Overall, P addition in the subalpine forest over 8 years influenced SOC composition through divergent alterations of plant- and microbial-derived C contributions, but did not shape SOC physical and chemical stability. Such findings may aid in accurately forecasting SOC dynamics and their potential feedbacks to climate change with future scenarios of increasing soil P availability in Earth system models.

Effects of Habitat Differences on Microbial Communities during Litter Decomposing in a Subtropical Forest

The differences between aquatic and terrestrial habitats could change microbial community composition and regulate litter decomposition in a subtropical forest, but the linkage remains uncertain. Using microbial phospholipid fatty acids (PLFAs), the litter decomposition associated with microbial organisms was monitored to characterize the differences of microbial communities in the forest floor, headwater stream, and intermittent stream. Habitat type did not significantly affect the concentrations of total PLFA. However, microbial community composition (fungi, G+ bacteria, and eukaryote) was significantly affected by the microenvironment among habitats. Compared with which in headwater stream, more individual PLFAs were identified in the natural forest floor and the intermittent stream during the whole decomposition period. The differences in individual PLFA concentrations were reflected in the forest floor and aquatic system in the early stage of litter decomposition, but they mainly reflected in the headwater stream and the intermittent stream in the later stage of litter decomposition. We linked the relationships between microbial community and litter decomposition and found that communities of decomposers drive differences in litter decomposition rate among habitats. Intriguingly, the microbial community showed the greatest correlation with the decomposition rate of litter in streams. These findings could contribute to the understanding of habitats difference on the microbial community during litter decomposition.

Changes in the Microbiological Properties of Soils along the Gradient of the Altitude Zone of Mount Kivaka in Eastern Fennoscandia, Russia

This study was conducted on the territory of the national park Paanayarvi, located in the taiga zone of the European north. The altitude zone common in the territory of the national park is up to 350 m above sea level. The purpose of this work is to study the microbiological and biochemical properties of soils formed under conditions of a gradient of altitude zonation. This work was performed for the first time in this territory. Based on the fatty acid composition of the cell walls of microorganisms, the composition and structure of the microbial community were determined by chemato-mass spectrometry. The dominant microbocenosis of soils of undisturbed territories was revealed. Changes in prokaryotes and microscopic fungi in the gradient of the altitude zone occur in different directions, which is consistent with the work of other researchers. The results suggest that the formation of microbocenosis of soils located in different conditions of the phytocenotic environment depends on the location of the site relative to the height. The latter determines the flow of solar energy into the ecosystem and the hydrothermal regime of soils. The data obtained can be used in monitoring global climate changes, will become the basis for the formation of a general conceptual basis for the functioning of microbial communities of soils of low-mountain landscapes.

The Potential Application of Natural Clinoptilolite-Rich Zeolite as Support for Bacterial Community Formation for Wastewater Treatment

The aim of this study was to investigate the use of natural zeolite as support for microbial community formation during wastewater treatment. Scanning electron microscopy (SEM), thermal decomposition and differential thermogravimetric curves (TGA/DGT) techniques were used for the physicochemical and structural characterization of zeolites. The chemical characterization of wastewater was performed before and after treatment, after 30 days of using stationary zeolite as support. The chemical composition of wastewater was evaluated in terms of the products of nitrification/denitrification processes. The greatest ammonium (NH4+) adsorption was obtained for wastewater contaminated with different concentrations of ammonium, nitrate and nitrite. The wastewater quality index (WWQI) was determined to assess the effluent quality and the efficiency of the treatment plant used, showing a maximum of 71% quality improvement, thus suggesting that the treated wastewater could be discharged into aquatic environments. After 30 days, NH4+ demonstrated a high removal efficiency (higher than 98%), while NO3+ and NO2+ had a removal efficiency of 70% and 54%, respectively. The removal efficiency for metals was observed as follows (%): Mn > Cd > Cr > Zn > Fe > Ni > Co > Cu > Ba > Pb > Sr. Analysis of the microbial diversity in the zeolite samples indicated that the bacteria are formed due to the existence of nutrients in wastewater which favor their formation. In addition, the zeolite was characterized by SEM and the results indicated that the zeolite acts as an adsorbent for the pollutants and, moreover, as a support material for microbial community formation under optimal conditions. Comparing the two studied zeolites, NZ1 (particle size 1−3 mm) was found to be more suitable for wastewater treatment. Overall, the natural zeolite demonstrated high potential for pollutant removal and biomass support for bacteria community growth in wastewater treatment.

Diversity and Effect of Increasing Temperature on the Activity of Methanotrophs in Sediments of Fildes Peninsula Freshwater Lakes, King George Island, Antarctica

Global warming has a strong impact on polar regions. Particularly, the Antarctic Peninsula and nearby islands have experienced a marked warming trend in the past 50 years. Therefore, higher methane (CH₄) emissions from this area could be expected in the future. Since mitigation of these emissions can be carried out by microbial oxidation, understanding this biological process is crucial since to our knowledge, no related studies have been performed in this area before. In this work, the aerobic CH₄ oxidation potential of five freshwater lake sediments of Fildes Peninsula (King George Island, South Shetland Islands) was determined with values from 0.07 to 10 μmol CH₄ gdw^–1 day^–1 and revealed up to 100-fold increase in temperature gradients (5, 10, 15, and 20°C). The structure and diversity of the bacterial community in the sediments were analyzed by next-generation sequencing (Illumina MiSeq) of 16S rRNA and pmoA genes. A total of 4,836 ASVs were identified being Proteobacteria, Actinobacteriota, Acidobacteriota, and Bacteroidota the most abundant phyla. The analysis of the pmoA gene identified 200 ASVs of methanotrophs, being Methylobacter Clade 2 (Type I, family Methylococcaceae) the main responsible of the aerobic CH₄ oxidation. Moreover, both approaches revealed the presence of methanotrophs of the classes Gammaproteobacteria (families Methylococcaceae and Crenotrichaceae), Alphaproteobacteria (family Methylocystaceae), Verrucomicrobia (family Methylacidiphilaceae), and the candidate phylum of anaerobic methanotrophs Methylomirabilota. In addition, bacterial phospholipid fatty acids (PLFA) biomarkers were studied as a proxy for aerobic methane-oxidizing bacteria and confirmed these results. Methanotrophic bacterial diversity was significantly correlated with pH. In conclusion, our findings suggest that aerobic methanotrophs could mitigate in situ CH₄ emissions in a future scenario with higher temperatures in this climate-sensitive area. This study provides new insights into the diversity of methanotrophs, as well as the influence of temperature on the CH₄ oxidation potential in sediments of freshwater lakes in polar regions of the southern hemisphere.

Spatial and temporal variations in salt marsh microorganisms of the Wadden Sea

Salt marshes exist at the interface of the marine and the terrestrial system. Shore height differences and associated variations in inundation frequency result in altered abiotic conditions, plant communities, and resource input into the belowground system. These factors result in three unique zones, the upper salt marsh (USM), the lower salt marsh (LSM), and the pioneer zone (PZ). Marine detritus, such as micro- and macroalgae, is typically flushed into the PZ daily, with storm surges moving both salt marsh detritus and marine detritus into higher salt marsh zones. Microbial assemblages are essential for the decomposition of organic matter and have been shown to sensitively respond to changes in abiotic conditions such as oxygen supply and salinity. However, temporal and spatial dynamics of microbial communities of Wadden Sea salt marshes received little attention. We investigated the dynamics of soil microbial communities across horizontal (USM, LSM, and PZ), vertical (0-5 and 5-10-cm sediment depth), and temporal (spring, summer, and autumn) scales in the Wadden Sea salt marsh of the European North Atlantic coast using phospholipid fatty acid (PLFA) analysis. Our results show strong spatial dynamics both among salt marsh zones and between sediment depths, but temporal dynamics to be only minor. Despite varying in space and time, PLFA markers indicated that bacteria generally were the dominant microbial group across salt marsh zones and seasons, however, their dominance was most pronounced in the USM, whereas fungal biomass peaked in the LSM and algal biomass in the PZ. Only algal markers and the stress marker monounsaturated to saturated fatty acid ratio responded to seasonality. Overall, therefore, the results indicate remarkable temporal stability of salt marsh microbial communities despite strong variability in abiotic factors.

Applying cover crop residues as diverse mixtures increases initial microbial assimilation of crop residue-derived carbon

Increasing the diversity of crops grown in arable soils delivers multiple ecological functions. Whether mixtures of residues from different crops grown in polyculture contribute to microbial assimilation of carbon (C) to a greater extent than would be expected from applying individual residues is currently unknown. In this study, we used 13C isotope labelled cover crop residues (buckwheat, clover, radish, and sunflower) to track microbial assimilation of plant residue-derived C using phospholipid fatty acid (PLFA) analysis. We also quantified microbial assimilation of C derived from the soil organic matter (SOM) because fresh residue inputs also prime the decomposition of SOM. To consider the initial stages of residue decomposition, and preclude microbial turnover, we compared a quaternary mixture of residues with the average effect of their four components 1 day after incorporation. Our results show that the microbial biomass carbon (MBC) in the treatment receiving the mixed residue was significantly greater, by 132% (3.61 μg C g-1), than the mean plant residue-derived MBC in treatments receiving the four individual components of the mixture. However, there was no evidence that the mixture resulted in any additional assimilation of C derived from native SOM than the average observed in individual residue treatments. We surmise that, during the initial stages of crop residue decomposition, a greater biodiversity of residues increases microbial assimilation to a greater extent than would be expected from applying individual residues either due to faster decomposition or greater carbon use efficiency (CUE). This might be facilitated by functional complementarity in the soil microbiota, permitted by a greater diversity of substrates, reducing competition for any single substrate. Therefore, growing and incorporating crop polycultures (e.g., cover crop mixtures) could be an effective method to increase microbial C assimilation in the early stages of cover crop decomposition.

Highlights

The effect of mixing crop residues on assimilation of C by soil microbial biomass was investigated.The study is important due to recent interest in diverse cover crop mixtures for arable systems.Mixing crop residues enhanced the assimilation of plant residue-derived C into microbial biomass.Growing and incorporating cover crop polycultures may enhance C storage in arable soils.