Phospholipid Fatty Acid Biomarkers Research Articles

Chemical composition of soil carbon is governed by microbial diversity during understory fern removal in subtropical pine forests

Understory vegetation has an important impact on soil organic carbon (SOC) accumulation. However, little is known about how understory vegetation alters soil microbial community composition and how microbial diversity contributes to SOC chemical composition and persistence during subtropical forest restoration. In this study, removal treatments of an understory fern (Dicranopteris dichotoma) were carried out within pine (Pinus massoniana) plantations restored in different years in subtropical China. Soil microbial community composition and microbial diversity were measured using phospholipid fatty acids (PLFAs) biomarkers and high-throughput sequencing, respectively. The chemical composition of SOC was also measured via solid-state 13C nuclear magnetic resonance (13C NMR). Our results showed that fern removal decreased alkyl C by 4.2 % but increased O-alkyl C by 15.6 % on average, leading to a decline of alkyl C/O-alkyl C ratio, suggesting altered chemical composition of SOC and lowered SOC recalcitrance without fern. Fern removal significantly lowered the fungi-to-bacteria ratio, and it also reduced fungal and bacterial diversity. Partial correlation analysis revealed that soil nitrogen availability was a key factor influencing microbial diversity. Bacterial diversity showed a close relationship with the Alkyl C/O-alkyl C ratio following fern removal. Furthermore, the microbial community structure and bacterial diversity were responsible for 18 % and 55 % of the explained variance in the chemical composition of SOC, respectively. Taken together, these analyses jointly suggest that bacterial diversity exerts a greater role than microbial community structure in supporting SOC persistence during understory fern removal. Our study emphasizes the significance of understory ferns in supporting microbial abundance and diversity as a means of altering SOC persistence during subtropical forest restoration.

Long-term integrated crop-livestock grazing stimulates soil ecosystem carbon flux, increasing subsoil carbon storage in California perennial agroecosystems

The strategic use of ruminant grazing in perennial cropland is steadily increasing throughout Mediterranean perennial agroecosystems. Integrated sheep-vineyard (ISV) management, where small ruminant livestock graze on understory vegetation, is viewed by some practitioners as a feasible transition opportunity to facilitate less petrochemically intensive vineyard understory management. However, our knowledge of soil carbon dynamics associated with grazing in perennial integrated crop-livestock (ICL) agroecosystems is notably limited, especially within Mediterranean climate contexts. Here, we use a series of on-farm paired surveys to assess soil ecosystem habitat and resource conditions related to SOC flux and storage in vineyards utilizing sheep-integration (ISV) and conventional understory management techniques (CONV). Our results show that long-term grazing increased the quantity of active, labile, and soluble carbon (C) within ISV soils, with much higher quantities of microbial biomass carbon (MBC). Vineyard soils with sheep grazing also showed increases in phospholipid fatty acid (PLFA) biomarkers, particularly amongst core functional groups related to decomposition. Soil microbial communities under ISV had higher C mineralization rates as well as higher carbon use-efficiency, as indicated by less CO2-C respired relative to the size of the MBC pool. Whereas inorganic soil nitrogen (N) and phosphorous (P) were also higher under ISV, microbial communities showed distinct metabolic investment strategies related to nutrient acquisition, with lower P-cycling enzyme activity and higher N-cycling enzyme activity. Additionally, ISV resulted in an increase in subsoil SOC storage, including higher quantities of physicochemical stabilization in the mineral-associated organic carbon (MAOC) pool of the deepest measured subsoil layer (30–45 cm). We observed no differences in soil structure indicators between treatments nor differences in the carbon fractions associated with four distinct aggregate size categories. We propose a framework to explain observed shifts in SOC dynamics of perennial ICL systems that include i) deposition of C and nutrient inputs with higher lability and solubility; ii) ruminant-induced decoupling of C from N and P, resulting in increased nutrient bioavailability; and iii) altered soil microbial metabolic strategies with more efficient biomass accumulation. These findings show strong potential of strategically applied ICL grazing to enhance soil functioning and increase SOC storage in Mediterranean perennial agroecosystems.

Effect of two broad-spectrum fungicides on the microbial communities of a soil subjected to different degrees of water erosion

The impact of both fungicide and water erosion on soil microbial communities has been little studied, and far less in subhumid-dry climates. To help fill this knowledge gap, we evaluated the influence of two broad-spectrum fungicides applied to soil subjected to different degrees of water erosion on microbial population and function. Soil samples were taken from an experimental site under three water erosion levels: an agricultural land subjected to minimum water erosion by terrace farming (MIN), an agricultural land subjected to moderate water erosion without terrace farming (MOD), and a land with no water erosion control treatment (non-eroded, NON). Three dosages of both carbendazim and iprodione were applied to microcosms, and the responses of microbial community and function were examined after 30-day exposure. Phospholipid fatty acid (PLFA) analysis, soil enzyme activities, and microbial abundances estimated by quantitative real-time PCR (qPCR) were used to evaluate the impact of carbendazim and iprodione fungicides applied at three dosages on microbial community structure and enzyme activities. The lowest values of fluorescein diacetate hydrolase (FDA), dehydrogenase, urease, and glucosidase activities were registered in soil under moderate erosion, while the highest ones were observed in non-eroded soils. Both carbendazim and iprodione decreased C- and P-related activities, even when those fungicides were applied at field rate doses. Thus, phosphomonoesterase, glucosidase, and xylosidase in soil treated with fungicides applied at recommended field rate decreased by 46 %, 61 %, and 34 % compared to soil without fungicide application. The lowest values of PLFA biomarkers for Gram-positive bacteria, Gram-negative bacteria, and arbuscular mycorrhizal fungi were registered in soils treated with the highest dose of both carbendazim and iprodione. Thus, Gram-positive bacteria, Gram-negative bacteria, arbuscular mycorrhizal fungi, and fungal PLFA biomarkers in soils without fungicide application were about 36 %, 3 %, 47 %, and 82 % higher than those soils treated with the highest doses of fungicides, respectively. In addition, the highest doses of fungicide application tended to greater decrease total PLFAs in both non-eroded and minimum eroded compared to moderate eroded soils. Similarly, the response of bacterial and fungal populations to fungicide treatment was more pronounced in non-eroded soils than in eroded soils. This study illustrates how the interactions between fungicides and water erosion levels affect soil enzyme activities, microbial abundances, and microbial community structure in agroecosystems.

Soil Microbial Composition and Soil Health of Reverse-Osmosis-Concentrate and Brackish-Groundwater Irrigated Soils in Southern New Mexico

The phospholipid fatty acid method was used to determine the shifts in microbial biomass due to irrigation with reverse-osmosis (RO) concentrate (or highly saline reject water) and brackish groundwater (BGW). In this greenhouse study, RO concentrate and BGW were applied to irrigate pecan trees for 8 months for two consecutive seasons. The objectives of the study were to (i) evaluate how irrigation with RO concentrate and BGW impacts soil microbial composition in pecan rhizospheres using microbial phospholipid fatty acid (PLFA) biomarkers as indicators, and (ii) evaluate its implications on soil health. Three treatments of RO concentrate (EC = 8.0 dS/m), BGW (EC = 4.0 dS/m), and the city of Las Cruces’s water (EC = 0.8 dS/m) as a control were used to irrigate pecan trees. EC, pH, and organic matter (OM%) content of the soil samples were measured, and PLFA biomarkers for the microbial community were determined. Na-, Cl-, and K-ion concentrations were 26.16, 32.54, and 5.93 meq/L in 2017 and 25.44, 24.26, and 5.49 meq/L in 2018, respectively, in RO irrigation pots. For two seasons, gram-positive bacteria were dominant, while gram-negative bacteria were not detected in the second season. PLFA biomarkers of fungi were found among all three treatments in the first season; however, they appeared only with BGW in the second season. Actinomycetes were recorded in the first season while they were not seen in the second season. Increases in soil salinity and microbial shifts could have important implications for soil health. Irrigating with RO and BGW shifted the soil microbial composition; therefore, long-term irrigation with BGW and RO concentrate would be deleterious for pecan production and soil health.

Effects of tree diversity on soil microbial community in a subtropical forest in Southwest China

Soil microorganisms are crucial for biological diversity and ecosystem processes in terrestrial ecosystems. Plant diversity has been reported to have positive effects on microbial communities. However, further research is required to understand the complex mechanisms that regulate the interactions between plants and soil microorganisms, especially the corresponding variations in soil microbial communities under tree diversity gradients in natural forest ecosystems. Therefore, we conducted a field investigation in a natural subtropical forest and collected 45 soil samples to evaluate how the soil microbial biomass and community diversity (represented by phospholipid fatty acid biomarkers) responded to a tree diversity gradient as well as their associations with plant (root and litter) traits and soil variables. The contents of total PLFAs ranged from 86.4 to 325.5 nmol g−1 soil with an average of 183.2 ± 66.1 nmol g−1 soil across the 45 plots. Tree diversity significantly enhanced microbial biomass and decreased microbial diversity. Hierarchical partitioning analysis revealed that the soil substrates (including inorganic and organic nutrients) were the major determinants of microbial biomass. Structural equation models also demonstrated that the effects of tree diversity on the biomass and diversity of soil microbial communities were mainly dependent on soil substrates and soil water content, respectively. In addition, soil microorganisms may potentially metabolize relatively recalcitrant carbon components under low tree diversity, whereas they tended to utilize labile carbon sources under high tree diversity. Overall, these findings suggested that the soil microbial community biomass and diversity exhibited distinct changes along the tree diversity gradient, and highlighted the key role of soil substrates availability in controlling microbial biomass.

Sediment microbial community structure, enzymatic activities and functional gene abundance in the coastal hypersaline habitats

Salt marsh vegetation, mudflat and salt production are common features in worldwide coastal areas; however, their influence on microbial community composition and structure has been poorly studied and rarely compared. In the present study, microbial community composition (phospholipid fatty acid (PLFA) profiling and 16S rRNA gene sequencing (bacterial and archaeal)) and structure, enzymatic activities and abundance of functional genes in the sediments of salt ponds (crystallizer, condenser and reservoir), mudflat and vegetated mudflat were determined. Enzyme activities (β-glucosidase, urease and alkaline phosphatase) were considerably decreased in saltpan sediments because of elevated salinity while sediment of vegetated mudflat sediments showed the highest enzyme activities. Concentrations of total microbial biomarker PLFAs (total bacterial, Gram-positive, Gram-negative, fungal and actinomycetes) were the highest in vegetated mudflat sediments and the lowest in crystallizer sediments. Nonmetric-multidimensional scaling (NMDS) analysis of PLFA data revealed that the microbial community of crystallizer, mudflat and vegetated mudflat was significantly different from each other as well as different from condenser and reservoir. The most predominant phyla within the classified bacterial fractions were Proteobacteria followed by Firmicutes, Bacteroidetes and Planctomycetes, while Euryarchaeota and Crenarchaeota phyla dominated the classified archaeal fraction. Cyanobacterial genotypes were the most dominant in the condenser. Mudflat and vegetated mudflat supported a greater abundance of Bacteroidetes and Actinobacteria, respectively. The results of the present study suggest that salt ponds had significantly decreased the microbial and enzyme activities in comparison to mudflat and vegetated mudflat sediments due to very high salinity, ionic concentrations and devoid of vegetation. The present study expands our understanding of microbial resource utilization and adaptations of microorganisms in a hypersaline environment.

Effects of Different Chinese Hickory Husk Returning Modes on Soil Nutrition and Microbial Community in Acid Forest Soil

Chinese hickory (Carya cathayensis Sarg.) is an important economic forest in Southeastern China. A large amount of hickory husk waste is generated every year but with a low proportion of returning. Meanwhile, intensive management has resulted in soil degradation of Chinese hickory plantations. This study aims to investigate the effects of three Chinese hickory husk returning modes on soil amendment, including soil acidity, soil nutrition, and microbial community. The field experiment carried out four treatments: control (CK), hickory husk mulching (HM), hickory husk biochar (BC), and hickory husk organic fertilizer (OF). The phospholipid fatty acid (PLFA) biomarker method was employed to determine the soil microbial community. After one year of treatment, the results showed that: (i) HM and BC significantly increased soil pH by 0.33 and 1.71 units, respectively; (ii) HM, BC and OF treatments significantly increased the soil organic carbon, alkaline nitrogen, available phosphorous, and available potassium. The OF treatment demonstrated the most significant improvement in the soil nutrient; (iii) The soil microbial biomass significantly increased in the HM, BC and OF treatments, and all microbial groups showed an increasing trend. HM treatment increased the fungal/bacterial ratio (F/B). The OF treatment significantly decreased the Shannon-Wiener diversity (H’) and evenness index (J) of the microbial community (P < 0.05). Considering the treatments effects, costs, and ease of operation, our recommended returning modes of Chinese hickory husk are mulching and organic fertilizer produced by composting with manure.

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.

The Characteristics of Dissolved Organic Matter and Soil Microbial Communities in the Soils of Larix principis-rupprechtii Mayr. Plantations in the Qinling Mountains, China

Soil microorganisms and dissolved organic matter (DOM) play vital roles in nutrient cycling and maintaining plant diversity. The aim of this study was to clarify the relationship between DOM component characteristics and microbial community structure in the soil of Larix principis-rupprechtii Mayr. plantations. We quantified the responses of the soil microbial and DOM characteristics to stand age in a plantation forest ecosystem using phospholipid fatty acid (PLFA) analyses, ultraviolet-visible spectroscopy, and fluorescence spectroscopy. Three humic-like components and a fulvic-like component were identified from the soil samples, and humic-like substances were the dominant component of the soil DOM of the stands of different ages. The fluorescence index showed that the sources of soil DOM in the stands of different ages throughout the growth stages may be mostly plant residues, with very little contribution from microbial sources. Furthermore, the results demonstrated that stand age and growth season had a significant effect on the contents of the soil PLFA biomarkers of L. principis-rupprechtii Mayr. Additionally, significantly higher contents of different species of soil PLFA biomarkers were observed in the young forest (17a) than in the sapling forest (7a) and half-mature forest (27a), suggesting that stand age differences in the quality and quantity of larch litter and soil physicochemical characteristics affect the microbial community structure. Redundancy analysis (RDA) showed that changes in the soil DOM quality and components that were driven by growth season and stand age were the major drivers of variations in the soil microbial community structure in the study region. Overall, the seasonal variations in DOM quality and components may contribute to the variability of soil microorganisms, and the soil microbial responses to tree age will depend upon the provisioning of these resources.

Evaluating phytochemical and microbial contributions to atrazine degradation

The inclusion of warm-season grasses, such as switchgrass (Panicum virgatum) and eastern gamagrass (EG) (Tripsacum dactyloides), in vegetated buffer strips has been shown to mitigate herbicide contamination in runoff and increase herbicide degradation in soil. The mode of action by which buffer strip rhizospheres enhance herbicide degradation remains unclear, but microorganisms and phytochemicals are believed to facilitate degradation processes. The objectives of this study were to: 1) screen root extracts from seven switchgrass cultivars for the ability to degrade the herbicide atrazine (ATZ) in solution; 2) determine sorption coefficients (Kd) of the ATZ-degrading phytochemical 2-β-D-glucopyranosyloxy-4-hydroxy-1,4-benzoxazin-3-one (DBG) to soil and Ca-montmorillonite, and investigate if DBG or ATZ sorption alters degradation processes; and 3) quantify ATZ degradation rates and soil microbial response to ATZ application in mesocosms containing soil and select warm-season grasses. Phytochemicals extracted from the roots of switchgrass cultivars degraded 44–85% of ATZ in 16-h laboratory assays, demonstrating that some switchgrass cultivars could rapidly degrade ATZ under laboratory conditions. However, attempts to isolate ATZ-degrading phytochemicals from plant roots were unsuccessful. Sorption studies revealed that DBG was strongly sorbed to soil (Kd = 87.2 L kg−1) and Ca-montmorillonite (Kd = 31.7 L kg−1), and DBG driven hydrolysis of ATZ was entirely inhibited when either ATZ or DBG were sorbed to Ca-montmorillonite. Atrazine degradation rates in mesocosm soils were rapid (t0.5 = 8.2–11.2 d), but not significantly different between soils collected from the two switchgrass cultivar mesocosms, the eastern gamagrass cultivar mesocosm, and the unvegetated mesocosm (control). Significant changes in three phospholipid fatty acid biomarkers were observed among the treatments. These changes indicated that different ATZ-degrading microbial consortia resulted in equivalent ATZ degradation rates between treatments. Results demonstrated that soil microbial response was the dominant mechanism controlling ATZ degradation in the soil studied, rather than root phytochemicals.

Spatial and Temporal Changes of Soil Microbial Communities in Field Tomato Production as Affected by Anaerobic Soil Disinfestation

Anaerobic soil disinfestation (ASD) has been demonstrated as an effective alternative to pre-plant chemical soil fumigation (CSF) commonly used to control soilborne pathogens. However, the ASD effects on spatial and temporal changes in soil microbial communities remain poorly understood in production systems with low soilborne disease pressure. The objective of this study was to assess the influence of ASD treatments on soil microbial community composition at different soil depths during the spring tomato production season in Florida. Soil treatments included ASD using 6.9 m3 ha−1 of molasses with 11 Mg ha−1 of composted poultry litter (CPL) (ASD0.5), ASD with 13.9 m3 ha−1 of molasses and 22 Mg ha−1 CPL (ASD1.0), and chemical soil fumigation (CSF) using a mixture of 1,3-dichloropropene and chloropicrin. Soil microbial community composition was measured at soil depths of 0–15 and 15–30 cm using phospholipid fatty acid (PLFA) analysis at 0, 36, 76, and 99 days after transplanting (DAT). Fatty acid methyl esters were categorized into biomarker groups including total microbial biomass (TMB), G+ bacteria (G+), G− bacteria (G−), actinomycetes (Actino), arbuscular mycorrhizal fungi (AMF), protozoa, and general fungi (F). Soil concentrations of G+, Actino, F, AMF, and the ratio of F:bacteria (B) were significantly impacted by a soil treatment × soil depth × sampling time three-way interaction. All the microbial biomarkers were significantly affected by soil treatment × sampling depth two-way interactions except for protozoa and F:B ratio. Concentrations of TMB, Actino, AMF, F, G+, and G− bacteria were significantly increased in ASD treated soils at both 0–15 and 15–30 cm soil depths across different sampling times compared with CSF. In addition, the concentrations of G+ and G− bacteria, AMF, F, and TMB were higher at 0–15 vs. 15–30 cm soil depth under ASD treatments, whereas no soil depth differences were observed in CSF. Discriminant analysis further confirmed that soil microbial community composition was distinctly different in CSF compared with ASD treatments. The soil microbial profile was well-differentiated between the two soil depths under ASD treatments but not in CSF, while the enhancement of PLFA biomarkers by ASD decreased with increasing soil depth.

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.

Biochemical composition and function of subalpine shrubland and meadow soil microbiomes in the Qilian Mountains, Qinghai-Tibetan plateau, China.

Microorganisms participate in the soil biogeochemical cycle. Therefore, investigating variations in microbial biomass, composition, and functions can provide a reference for improving soil ecological quality due to the sensitivity of microorganisms to vegetation coverage changes. However, the differences in soil microorganisms between shrubland and meadow have not been investigated in ecologically vulnerable subalpine areas. This study aimed to investigate the biochemical composition and functions of the soil microbial community under two shrublands and a meadow at high altitudes (3,400–3,550 m). Three sites under two shrublands, Rhododendron thymifolium (RHO) and Potentilla fruticosa (POT), and one meadow dominated by Kobresia myosuroides (MEA), were selected on the southern slope of the Qilian Mountains on the northeastern edge of the Qinghai–Tibetan Plateau, China. Soil physicochemical properties, the microbial community composition expressed by the phospholipid fatty acid (PLFA) biomarker, and enzyme activities were analyzed as well as their relationships. The results showed that water holding capacity and the soil carbon, nitrogen, and potassium content in RHO and POT were higher than those in the MEA. Moreover, the soil active carbon, dissolved organic carbon, total nitrogen, and dissolved total nitrogen content in RHO were higher than those in POT. The abundance of total PLFAs, bacteria, and fungi beneath the shrublands was considerably higher than that in the MEA. The PLFA abundance in RHO was significantly higher than that in POT. The fungal-to-bacterial ratio of RHO and POT was significantly higher than that in the MEA. The activities of β-glucosidase, cellobiohydrolase, and leucine aminopeptidase were the highest in RHO among the three vegetation types, followed by POT and MEA. The redundancy analysis indicated that the biochemical composition of the soil microorganisms and enzyme activities were driven by total nitrogen, dissolved organic carbon, water holding capacity, and soil organic carbon. Therefore, shrublands, which have higher biomass, can improve soil moisture status, increase soil carbon and nitrogen content (especially active carbon and active nitrogen), and further increase the abundance of total PLFAs, bacteria, and fungi. The increase of microbial biomass indirectly enhances the activity of relevant soil enzymes. The variations in PLFA abundance and enzyme activities can be attributed to shrub species, especially evergreen shrubs, which create more favorable conditions for soil microorganisms. This study provides a theoretical basis for investigating the soil biogeochemical cycle and a scientific basis for soil management and vegetation restoration in the subalpine regions.

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.

Fungi determine increased soil organic carbon more than bacteria through their necromass inputs in conservation tillage croplands

Stover mulching over no-till soil is regarded as a promising practice to increase soil organic carbon (SOC) in croplands against climate change. Microbial necromass is a significant source of SOC stock and unequivocally controlled by the microbial community. Yet, a complete link that spans from agricultural practices to microbial community features, to soil necromass C, and eventually to SOC is poorly understood. Here, we conducted a 10-y corn field experiment with five treatments, which included conventional tillage (CT), no-tillage without stover (NT–0), and no-tillage with low, medium, and high amounts of stover mulching (NT–low, NT–medium, and NT–high) in a Molisol of northeastern China. We investigated the stocks and changes in total SOC and its microbial necromass C along a soil depth down to 40 cm, and we evaluated how SOC dynamics and stabilization processes were associated with microbial community features. We characterized microbial community diversity and structure using 16S rRNA and internal transcribed spacer (ITS) sequencing, and we characterized microbial biomass and necromass using phospholipid fatty acid and amino sugar biomarkers. Compared with conventional tillage, no-tillage with medium and high amounts of stover mulching increased SOC stocks in the upper 0–40 cm of soil by > 0.4% per year. No-tillage treatments (without and with stover) had almost no effect on the proportion of total microbial necromass C to SOC, but greatly modified the ratio of fungal necromass C to bacterial necromass C, which increased in top layers (0–5 cm) and decreased in deep layers (10–40 cm). SOC was governed mainly by fungal necromass C, which was correlated positively with fungal biomass. Fungal necromass C, not bacterial necromass C, was more closely associated with microbial community composition. Our results suggested that no-tillage with medium stover mulching was the optimal treatment to achieve the best trade-off between stover input and SOC storage. Differentiating microbial C pools from total SOC and, notably, separating fungal and bacterial necromass C pools can refine our mechanistic understanding of SOC storage as well as its association with microbial biota.

亚热带红壤区森林土壤剖面微生物残体碳分布及影响因素

土壤剖面中20cm以下土壤有机碳（SOC）储量占土壤剖面总SOC储量50%左右，由于土壤微生物残体碳（MRC）是稳定土壤碳库的重要来源，因此研究土壤剖面中MRC对SOC的贡献对于评估土壤碳储量具有重要意义。然而，目前关于MRC含量及其对SOC贡献的研究多数集中在土壤表层，在土壤剖面和母质中尚不清楚。选取江西省千烟洲亚热带典型森林红壤剖面，通过氨基糖与磷脂脂肪酸（PLFA）微生物标志物分析方法，分析红壤剖面和母质中MRC的影响机制及其对SOC贡献的分布特征。研究结果表明：（1）MRC含量随着土壤剖面深度增加而显著降低（P<0.05），在整个土壤剖面中，细菌MRC对SOC贡献为6%-12%，真菌MRC对SOC贡献为12%-36%，MRC对SOC贡献为18%-46%。从土壤表层至母质，真菌MRC对SOC贡献高于细菌MRC。（2）结构方程模型结果表明，在土壤剖面中，MRC含量主要受到微生物-PLFA含量、容重和溶解态有机碳含量的影响。研究量化了红壤剖面中MRC对SOC的贡献，表明在20cm以下土壤及母质中，微生物残体碳对红壤地区生态系统碳库具有重要贡献。;In soil profiles, soil organic carbon (SOC) storage beneath 20cm accounts for about 50% of the total SOC storage in the terrestrial ecosystem. Microbial residue carbon (MRC) is considered as an important constituent of persistent soil organic carbon. It is important to learn the role of MRC for soil carbon storage in deep soil as the main source of soil stable carbon pool. Until now, most studies involving MRC content and the contribution of MRC to SOC have mainly focused on surface soil, but seldom in deep soil and parent material. In this study, we selected typical red soil profiles in Qianyanzhou, Jiangxi province in subtropical region. We measured the microbial biomarkers of amino sugars and phospholipid fatty acids (PLFAs) which represent microbial residue carbon content and living microbial biomass content, respectively. The objective of the study was to analyze the influence factors of MRC and to quantify the contributions of MRC to SOC along the soil profiles from the surface to parent material. The results showed that (1) bacterial residue carbon (MRC_B), fungal residue carbon (MRC_F) and MRC contents decreased significantly with soil depth (P<0.05), and were about 0.08, 0.18, 0.25 g/kg at the parent material, respectively. The contributions of MRC to SOC along the soil profiles remained unchanged because of the same variation trend of MRC and SOC contents. Along the whole soil profiles, the contributions of MRC_B, MRC_F and MRC to SOC were about 6%-12%, 12%-36% and 18%-46%, respectively. The contribution of MRC_F to SOC was higher than that of MRC_B to SOC from surface soil to parent material. This may be caused by different components of cell walls in bacteria and fungi. The chitin in cell wall of fungi is more difficult to decompose than peptidoglycan in cell wall of bacteria. In addition, MRC_F could have more physical protection than MRC_B by soil aggregates since extracellular mycelia and polysaccharides are involved in the formation of soil aggregates. (2) The structural equation model showed that MRC content was largely determined by microbial biomass content of PLFA biomarkers, soil bulk density (Db) and dissolved organic carbon (DOC) content in the soil profiles, while Db and DOC indirectly influenced but microbial-PLFA content directly influenced the MRC content. Our study quantified the contribution of MRC to SOC along the soil profile and emphasized the contribution of MRC to the formation of ecosystem carbon pool beneath 20cm and in the parent material in red soil region.

Foliar application of fertilizers and biostimulant has a strong impact on the olive (Olea europaea) rhizosphere microbial community profile and the abundance of arbuscular mycorrhizal fungi

Many studies on biostimulants and nutrient-based fertilizers of olive trees have been focused on the ability of these products to increase olive productivity and ameliorate oil quality. However, little information is available on their effects on rhizosphere microbial communities; whereas it is well known that microorganisms associated with plants play a key role on the productivity and the health of their host. The aim of this study was to evaluate the effects of foliar application of a biostimulant and nutrient fertilizers on photosynthesis, carbohydrate profile of the roots and soil microbial community structure. Specific attention was paid to arbuscular mycorrhizal (AM) fungi. The phospholipid fatty acid (PLFA) 16:1ω5 and the neutral lipid fatty acid (NLFA)16:1ω5 in the roots (intraradical mycelium) and in the soil (extraradical mycelium) were used as biomarkers for AM fungi. Experimentation consists of the annual foliar application of six nutrient-based treatments during two successive growing seasons: TC (untreated trees), T1 (nitrogen-based fertilizer), T2 (biostimulant rich in boron, magnesium, sulfur, manganese and amino acids), T3 (products rich in phosphorus, potassium and boron), T4 (product rich in phosphorus, calcium and zinc), T12 (application of T1 and T2) and T1234 (application of T1, T2, T3 and T4). At the end of the experiment, statistical analysis revealed a significant modification of macronutrient and micronutrient profiles of olive leaves, which caused a significant increase of photosynthesis and induced quantitative changes in the most of individual root sugars, essentially the translocated forms of sugars (sucrose and mannitol). Foliar application of fertilizers and biostimulant increased the PLFA biomarkers indicative of Gram-positive bacteria (i15:0, i16:0), Gram-negative bacteria (16:1ω7, 16:1ω9, cy17:0, 18:1ω7 and cy19:0) and actinobacteria (10Me16:0). The level of NLFA 16:1ω5 in both the rhizosphere and roots, increased significantly under foliar fertilization, however the level of PLFA 16:1ω5 did not appear to be significantly influenced, suggesting that spore and vesicle formation was more sensitive to foliar fertilization than the hyphae development. The NLFA 16:1ω5/PLFA 16:1ω5 ratio, in the roots of olive trees, showed a significant increase, indicating that AM fungi allocated high carbon to storage structures following foliar fertilization. Our study provides evidence that foliar fertilization induces rapid changes in specific microbial groups, which in turn increase the rhizosphere carbon metabolism.

Phospholipid fatty acid (PLFA) analysis as a tool to estimate absolute abundances from compositional 16S rRNA bacterial metabarcoding data

Microbial biodiversity monitoring through the analysis of DNA extracted from environmental samples is increasingly popular because it is perceived as being rapid, cost-effective, and flexible concerning the sample types studied. DNA can be extracted from diverse media before high-throughput sequencing of the prokaryotic 16S rRNA gene is used to characterize the taxonomic diversity and composition of the sample (known as metabarcoding). While sources of bias in metabarcoding methodologies are widely acknowledged, previous studies have focused mainly on the effects of these biases within a single substrate type, and relatively little is known of how these vary across substrates. We investigated the effect of substrate type (water, microbial mats, lake sediments, stream sediments, soil and a mock microbial community) on the relative performance of DNA metabarcoding in parallel with phospholipid fatty acid (PLFA) analysis. Quantitative estimates of the biomass of different taxonomic groups in samples were made through the analysis of PLFAs, and these were compared to the relative abundances of microbial taxa estimated from metabarcoding. Furthermore, we used the PLFA-based quantitative estimates of the biomass to adjust relative abundances of microbial groups determined by metabarcoding to provide insight into how the biomass of microbial taxa from PLFA analysis can improve understanding of microbial communities from environmental DNA samples. We used two sets of PLFA biomarkers that differed in their number of PLFAs to evaluate how PLFA biomarker selection influences biomass estimates. Metabarcoding and PLFA analysis provided significantly different views of bacterial composition, and these differences varied among substrates. We observed the most notable differences for the Gram-negative bacteria, which were overrepresented by metabarcoding in comparison to PLFA analysis. In contrast, the relative biomass and relative sequence abundances aligned reasonably well for Cyanobacteria across the tested freshwater substrates. Adjusting relative abundances of microbial taxa estimated by metabarcoding with PLFA-based quantification estimates of the microbial biomass led to significant changes in the microbial community compositions in all substrates. We recommend including independent estimates of the biomass of microbial groups to increase comparability among metabarcoding libraries from environmental samples, especially when comparing communities associated with different substrates.

The effect of tillage management on microbial functions in a maize crop at different slope positions

Determining whether agricultural soils act as sinks or sources of greenhouse gases (GHGs) requires the quantification of variations in the pools and fluxes of soil organic carbon (SOC) and nutrients, e.g. nitrogen (N), as well as the associated soil microbial responses. In this study, soil was collected from experimental plots of maize (Zea mays) under conventional, minimum or strip tillage treatments established in a sloping field (~10%) of loamy soil in SW England, UK, where maize had been cultivated conventionally for 12 years. Topsoil (0–10 cm) cores were collected from the top, mid, bottom and foot slope positions to investigate soil C, N and microbial properties. The impact of conventional management on potential GHG emissions was assessed by incubating soils collected from the top, mid and bottom slope positions from the conventional treatment. Contents of SOC and total N were greatest at the top slope position and soil mineral N (NO3−-N and NH4+-N) concentrations were greater at the bottom and foot slope positions in all treatments. Biomarker phospholipid fatty acids (PLFA) for Gram positive bacteria and fungi were relatively 13C-enriched at each slope position regardless of treatment, indicating preferential utilization of organic matter from maize (C4) rather than SOC (C3). Around 70% of carbon incorporated into total PLFA was derived from C3-SOC at the slope foot, indicating that more SOC older than 12 years was being mineralized at the depositional position. Effluxes of N2O and CO2, and total GHG emission were greatest from the incubated soils sampled from the bottom slope position, suggesting that conditions in depositional positions of regularly ploughed sloping arable fields may have increased the potential for mineralization and denitrification. We conclude that the C sink potential of the depositional positions of slopes may be diminished by coincidental GHG emissions.

The Effect of Botanicals with Nematicidal Activity on the Structural and Functional Characteristics of the Soil Nematode Community

We investigated the effects of three botanicals with nematicidal properties (anise-Pimpinella anisum, parsley-Petroselinum crispum, and rocket-Eruca sativa) on the soil nematode community, in terms of trophic structure and nematode genera composition. We compared effects with those of fluopyram (synthetic nematicide) and Nemagold (bionematicide). We assessed the role of time, by sampling 15 and 45 days after treatments and analyzing nematode genera and microbial phospholipid fatty acid biomarkers (PLFA). Soil incorporation of botanicals reduced plant parasitic nematodes, increased bacterivores, especially the enrichment opportunists and among them Rhabditis, having no effect on fungivores and non-parasitic plant feeders. Neither the number nor the composition and dominance hierarchy of nematode genera were affected. Nemagold did not induce any significant change, while fluopyram decreased both free-living and parasitic nematodes, but with no uniform effect against all genera. The least affected genus was the fungivorous Aphelenchus. While most microbial PLFAs increased with time, the abundances of nematode genera did not change, except the Meloidogyne incognita second stage juveniles, which emerged in soil only 45 days after treatments. The low enrichment index and high channel index values of the fluopyram soil samples indicated a stressful environment. The opposite was observed in the botanical treatments, especially parsley and rocket.