Composition Of Microbial Communities In Soil Research Articles

Soil Metaproteomics for Microbial Community Profiling: Methodologies and Challenges.

Soil represents a complex and dynamic ecosystem, hosting a myriad of microorganisms that coexist and play vital roles in nutrient cycling and organic matter transformation. Among these microorganisms, bacteria and fungi are key members of the microbial community, profoundly influencing the fate of nitrogen, sulfur, and carbon in terrestrial environments. Understanding the intricacies of soil ecosystems and the biological processes orchestrated by microbial communities necessitates a deep dive into their composition and metabolic activities. The advent of next-generation sequencing and 'omics' techniques, such as metagenomics and metaproteomics, has revolutionized our understanding of microbial ecology and the functional dynamics of soil microbial communities. Metagenomics enables the identification of microbial community composition in soil, while metaproteomics sheds light on the current biological functions performed by these communities. However, metaproteomics presents several challenges, both technical and computational. Factors such as the presence of humic acids and variations in extraction methods can influence protein yield, while the absence of high-resolution mass spectrometry and comprehensive protein databases limits the depth of protein identification. Notwithstanding these limitations, metaproteomics remains a potent tool for unraveling the intricate biological processes and functions of soil microbial communities. In this review, we delve into the methodologies and challenges of metaproteomics in soil research, covering aspects such as protein extraction, identification, and bioinformatics analysis. Furthermore, we explore the applications of metaproteomics in soil bioremediation, highlighting its potential in addressing environmental challenges.

Anaerobic biodegradation of perfluorooctane sulfonate (PFOS) and microbial community composition in soil amended with a dechlorinating culture and chlorinated solvents

Perfluorooctane sulfonate (PFOS), one of the most frequently detected per- and polyfluoroalkyl substances (PFAS) occurring in soil, surface water, and groundwater near sites contaminated with aqueous film-forming foam (AFFF), has proven to be recalcitrant to many destructive remedies, including chemical oxidation. We investigated the potential to utilize microbially mediated reduction (bioreduction) to degrade PFOS and other PFAS through addition of a known dehalogenating culture, WBC-2, to soil obtained from an AFFF-contaminated site. A substantial decrease in total mass of PFOS (soil and water) was observed in microcosms amended with WBC-2 and chlorinated volatile organic compound (cVOC) co-contaminants — 46.4 ± 11.0 % removal of PFOS over the 45-day experiment. In contrast, perfluorooctanoate (PFOA) and 6:2 fluorotelomer sulfonate (6:2 FTS) concentrations did not decrease in the same microcosms. The low or non-detectable concentrations of potential metabolites in full PFAS analyses, including after application of the total oxidizable precursor assay, indicated that defluorination occurred to non-fluorinated compounds or ultrashort-chain PFAS. Nevertheless, additional research on the metabolites and degradation pathways is needed. Population abundances of known dehalorespirers did not change with PFOS removal during the experiment, making their association with PFOS removal unclear. An increased abundance of sulfate reducers in the genus Desulfosporosinus (Firmicutes) and Sulfurospirillum (Campilobacterota) was observed with PFOS removal, most likely linked to initiation of biodegradation by desulfonation. These results have important implications for development of in situ bioremediation methods for PFAS and advancing knowledge of natural attenuation processes.

Freeze-thaw aged polyethylene and polypropylene microplastics alter enzyme activity and microbial community composition in soil

In cold regions, microplastics (MPs) in the soil undergo freeze-thaw (FT) aging process. Little is known about how FT aged MPs influence soil physico-chemical properties and microbial communities. Here, two environmentally relevant concentrations (50 and 500 mg/kg) of 50 and 500 µm polyethylene (PE) and polypropylene (PP) MPs treated soils were subjected to 45-day FT cycles (FTCs). Results showed that MPs experienced surface morphology, hydrophobicity and crystallinity alterations after FTCs. After 45-day FTCs, the soil urease (SUE) activity in control (MPs-free group that underwent FTCs) was 33.49 U/g. SUE activity in 50 µm PE group was reduced by 19.66 %, while increased by 21.16 % and 37.73 % in 500 µm PE and PP groups compared to control. The highest Shannon index was found in 50 µm PP-MPs group at 50 mg/kg, 2.26 % higher than control (7.09). Compared to control (average weighted degree=8.024), all aged MPs increased the complexity of network (0.19–1.43 %). Bacterial biomarkers of aged PP-MPs were associated with pollutant degradation. Aged PP-MPs affected genetic information, cellular processes, and disrupted the biosynthesis of metabolites. This study provides new insights into the potential hazards of MPs after FTCs on soil ecosystem in cold regions.

Field application of hydroxyapatite and humic acid for remediation of metal-contaminated alkaline soil.

The quality of soil is essential for ensuring the safety and quality of agricultural products. However, soils contaminated with toxic metals pose a significant threat to agricultural production and human health. Therefore, remediation of contaminated soils is an urgent task, and humic acid (HA) with hydroxyapatite (HAP) materials was applied for this study in contaminated alkaline soils to remediate Cd, Pb, Cu, and Zn. Physiochemical properties, improved BCR sequential extraction, microbial community composition in soils with superoxide dismutase (SOD), peroxidase (POD), and chlorophyll content in plants were determined. Among the studied treatments, application of HAP-HA (2:1) (T7) had the most significant impact on reducing the active forms of toxic metals from soil such as Cd, Pb, Cu, and Zn decreased by 18.59%, 9.12%, 11.83%, and 3.33%, respectively, but HAP and HA had a minor impact on metal accumulation in Juncao. HAP (T2) had a beneficial impact on reducing the TCleaf/root of Cd, Cu, and Zn, whereas HAP-HA (T5) showed the best performance for reducing Cd and Cu in EFleaf/soil. HAP-HA (T5 and T7) showed higher biomass (57.3%) and chlorophyll (17.9%), whereas HAP (T4) showed better performance in POD (25.8%) than T0 in Juncao. The bacterial diversity in soil was increased after applying amendments of various treatments and enhancing metal remediation. The combined application of HAP and HA effectively reduced active toxic metals in alkaline soil. HAP-HA mixtures notably improved soil health, plant growth, and microbial diversity, advocating for their use in remediating contaminated soils.

The Effect of Conventional and Conservative Tillage Systems on Microbial Community Composition and Physiological Activity in Soils from Bărăgan Plain

The paper aimed to present the results of research carried out on size, taxonomic composition and physiological activity of soil microbiota for assessing the effect of classic (conventional) and conservative (minimum tillage) agriculture systems applied in a zone affected by aridification from Bărăgan Plain. Significant differences concerning the quantitative parameters characterizing the bacterial and fungal communities from the two soil systems of tillage have been evidenced. Total counts of bacteria doubled and total counts of fungi was with one order of magnitude higher in soil minimum-tilled than in soil under conventional tillage system. Soil respiration values registered for both conservative and conventional systems are considered to characterize high levels of microbial physiological activities, with slightly higher values for minimum tillage system application than for conventional system. The beneficial effect of conservative system was evidenced by higher values of diversity indices registered for both bacterial and, especially fungal communities, as compared with those characterizing the communities from soil under conventional tillage system. The minimum tillage system favoured the increasing of abundance and diversity of actinomycetes, the dominance of Pseudomonas and Bacillus bacterial species and fungal species belonging to genera Aspergillus, Trichoderma, Mortierella and Paecilomyces in composition of soil microbiota, with multiple roles in main soil processes: decomposition of vegetal residues, synthesis of humus precursors, carbon sequestration, alleviation of various abiotic stress (drought, salinity), increasing accessibility of nutrients for plants, yields, biocontrol of plant pathogens.

Plant residues do not have an immediate impact on soil bacterial community composition and abundance

AbstractPlant residues are often used as soil amendments in laboratory experiments, but they can reportedly release compounds interfering with soil DNA extraction and subsequent molecular biological analyses. Theoretically, for accurate comparison of microbial community composition in soils with and without added plant residues after a period of incubation, no significant difference at the beginning of the experiment is required between the amended and unamended control soils. We mixed plant residue into soil and immediately (within 10 min) commenced DNA extraction, and then performed 16S rRNA gene sequencing and quantitative PCR (qPCR) to determine bacterial community composition and abundance. Soil without plant residue addition served as a control. Five commonly used DNA extraction kits, 16S rRNA gene primer pairs, and soils, and two types (rice straw and alfalfa shoots) and three addition rates (2%, 4%, and 6%; w/w) of plant residue, were tested. In all cases, we found no significant difference in measured bacterial community composition or abundance between the treatments with and without added plant residue.

Carbon substrate selects for different lineages of N2O reducing communities in soils under anoxic conditions

Agricultural soils are a main source of nitrous oxide (N2O), a potent greenhouse gas and the dominant ozone-depleting substance emitted to the atmosphere. The only known sink of N2O in soil is the microbial reduction of N2O to N2. Carbon (C) availability is a key factor in determining microbial community composition in soil. However, its role in shaping the structure of N2O reducing communities in soil is unexplored. In this study, a microcosm experiment was set up in which two arable soils with contrasting edaphic properties were incubated anaerobically for 83 days with four different C substrates: glucose, acetate, hydroxyethylcellulose (HEC) and mixture of the three. We show that the effect of C addition on the abundance and diversity of clade I and clade II nosZ genes, encoding different variants of the N2O reductase, varies across the different C substrates differently in contrasting soil types, yet still plays an important role in selecting specific taxa of N2O reducers under denitrifying conditions. We observed an increase of betaproteobacterial clade I and II N2O reducing species with addition of HEC, whereas alphaproteobacterial clade I species and clade II species within other Proteobacteria and Bacteriodetes were associated with glucose and acetate. These results show that specific C-substrates select for certain lineages of nitrous oxide reducers and influence patterns of niche partitioning within clades of N2O reducers, whereas other soil factors drive differences between clade I and II nosZ communities.

Impact of cropping systems on pedogenic distribution and transformations of micronutrients, plant accumulation and microbial community composition in soils: a review

Impact of cropping systems on pedogenic distribution and transformations of micronutrients, plant accumulation and microbial community composition in soils: a review

Reductive soil disinfestation with biochar amendment modified microbial community composition in soils under plastic greenhouse vegetable production

Reductive soil disinfestation (RSD) and biochar amendment are considered sustainable management practices to improve degraded vegetable soil. However, the combined effects of these two remediation methods on soil microbial communities and vegetable yields remain unclear. In the present field study, the interactive impacts of conventional RSD treatment and biochar were tested in plastic greenhouse soils under a continuous vegetable cultivation system. Six treatments consisted of different management practices: soil untreated (CK), soil amended with biochar (BC), soil flooded (SF), soil flooded and mulched with plastic film (SFM), soil amended with alfalfa residue, flooded and mulched with plastic film (RSD), and soil amended with alfalfa residue plus biochar, flooded and mulched with plastic film (RSD+BC). Analysis of the soil samples collected at 0–20 cm for a range of physicochemical and microbial properties revealed that both RSD and RSD+BC treatments decreased soil nitrate (NO3-) concentrations while increasing soil pH, ammonium (NH4+), dissolved organic carbon (DOC), and the low-valent ion (Fe2+, Mn2+) concentrations (P < 0.05). Unlike the BC, SF and SFM treatments, the RSD and RSD+BC treatments decreased the bacterial and fungal diversity (P < 0.05) compared to the CK, and altered microbial community composition. The RSD treatment significantly reduced the relative abundance of genus Fusarium while increasing the relative abundances of genera Bacillus and Clostridium, and the increase was more evident in the RSD+BC treatment, suggesting the potential of the latter to suppress pathogenic fungi while increasing beneficial bacteria. The structural equation model revealed the key role of soil redox potential (Eh) and NH4+ concentration in the regulation of microbial community composition. Furthermore, BC, RSD, and RSD+BC treatments increased pepper yield by 27.4%, 55.3% and 44.4%, respectively, compared to CK. The yield of pepper was positively correlated with the contents of DOC, NH4+, and the relative abundance of Bacillus and Clostridium in soil (P < 0.01), and negatively correlated with NO3- and relative abundance of Fusarium (P < 0.05). This study provides evidence for the efficiency of the combined application of RSD and biochar to amend the quality of degraded soils in plastic sheds under continuous cultivation.

Biowaste compost amendment modifies soil biogeochemical cycles and microbial community according to aggregate classes

The use of biowaste compost as soil organic amendment is of great interest for soil recovery. However, there is little knowledge of detailed effects on chemical, microbial, and biochemical properties in different soil compartments (aggregate classes) following long-term amendment with biowaste compost. We studied the distribution of soil organic carbon (SOC), total nitrogen (TN), soil microbial biomass (SMB), microbial community composition and activity in bulk soils and in three water stable aggregate classes (>250, 250–53, and <53 μm), after seven years of different fertilization treatments: biowaste compost (Com), mineral NPK fertilizers (Min), biowaste compost with half-dose N fertilizer (ComN), and no fertilizers as control (Cnt). Microbial biomass was assessed through a double-stranded DNA (dsDNA) based method and enzyme activities were determined using a microplate-based fluorometric assay. Denaturing gradient electrophoresis (DGGE) fingerprinting analysis was used to study the composition of both fungal and bacterial communities. Com and ComN treatments improved significantly SOC, TN and SMB in bulk soils and in all aggregate sizes. Composition of fungal and bacterial communities shifted with biowaste compost, more in soil aggregates than in bulk soils. To this change of microbial community composition in soil aggregates, corresponded a response of enzymes activities to fertilization treatments depending on aggregate size. Com treatment caused the highest enzyme activity in microaggregates (250–53 μm), whereas ComN and Min showed, in general, a higher activity in silt plus clay sized aggregates (<53 μm). The enzymes involved in biogeochemical cycle of P, with the exception of the phytase, displayed the lowest activity in macroaggregates (>250 μm), suggesting that the intensity of this cycle is lower in this soil niche; however, they increased with C accumulation due to both biowaste compost treatments. Furthermore, fungal diversity and richness decreased with fertilization treatments in all fraction except in macroaggregates. Thus, soil aggregates regulated the feedback of chemical, biochemical and microbial properties in response to soil fertilization strategies.

Degradation of polyethylene plastic in soil and effects on microbial community composition

Plastics pollution in global soil systems is becoming a severely global issue and potential threat to terrestrial ecosystem serves and human health. Herein, in order to determine the degradability and ecological effects of polyethylene (PE) films, we measured the weight loss and characterization of PE films and analyzed variation in microbial community. The results of weight loss, SEM and FTIR spectra exhibited that PE films had unique degradation performance under different conditions. Simultaneously, we investigated the effects of PE films on the microbial community, and the microbiota colonizing on plastics. PE films may change the soil microbial community composition in soil, and hold the post of unique matrix for microbial colonization. These results indicate that the degradation of PE films and microbial community composition in soil can be affected by different conditions (soil layer, time and plants). By assessing the alteration of microbial community composition and PE films in soil, this work will contribute to enhance our understanding on the potential risks of plastics on soil ecosystems and provide a scientific basis for understanding the ecological effect of plastics on soil functions.

Effects of substrate quality on carbon partitioning and microbial community composition in soil from an agricultural grassland

The use of organic amendments, including livestock slurry, in intensive grassland soils may result in a temporary increase or decrease in soil organic matter (SOM) mineralisation through microbial activity (positive or negative priming effect, PE). However, the effects of applying organic amendments of different complexity on the activity and composition of the microbial community, as well as on PE, in temperate grassland soils remain unclear. In this study, we hypothesised that the complexity of carbon (C) compounds added to the soil via livestock slurry and in carbohydrate amendments would significantly affect both the partitioning of C and the composition of the soil microbial community. We also hypothesised that applying slurry that had received a biological additive would significantly alter the partitioning of C within the soil and the soil microbial community, compared to an unamended slurry. Microbial community structure, based on phospholipid fatty acid (PLFA) analysis, microbial respiration, and uptake into microbial biomass of 14C-glucose, 14C-glucose-6-phosphate (G6P), and 14C-cellulose, alongside livestock slurry amended or not amended with a biological additive, were investigated in laboratory incubations to test these hypotheses. Both 14C mineralisation and 14C biomass uptake declined significantly as the complexity of the carbohydrate compound added to soil increased (glucose > G6P > cellulose), with the incorporation of C into microbial biomass exceeding respiration of C as CO2 for each compound. The soil microbial community structure was dominated by bacteria over fungi in all treatments through time, with a prevalence of gram-negative over gram-positive bacteria. Our data indicate that adding slurry to soil alongside carbohydrate compounds decreased microbial biosynthesis and the cumulative respiration of carbohydrate compounds, compared to treatments in which slurry was not applied. Our study also indicates that the use of biological additives during slurry storage increased 14C biomass uptake following application of slurry to agricultural grasslands, thus suggesting that biological additives have the potential to enhance soil fertility.

Response of microbial community composition in soils affected by coal mine exploitation

Surface mining activities, despite their benefits, lead to the deterioration of local and regional environmental quality and play a role in global ecosystem pollution. This research aimed to estimate the culturable microbial population structure at five locations near the opencast coal mine "Kakanj" (Bosnia and Herzegovina) via agar plate and phospholipid fatty acids (PLFA) method and to establish its relationship to the physical and chemical properties of soil. Using the ICP-OES method, the heavy metal pollution of all examined locations (overburden, former grass yard, forest, arable soil, and greenhouse) was observed. Substantial variations among the sites regarding the most expressed indicators of heavy metal pollution were noted; Cr, Pb, Ni, and Cu content ranged from 63.17 to 524.47, 20.57 to 349.47, 139.13 to 2785.67, and 25.97 to 458.73mg/kg, respectively. In the overburden sample, considerable low microbial activity was detected; the bacterial count was approximately 6- to 18-fold lower in comparison with the other samples. PLFA analysis showed the reduction of microbial diversity, reflected through the prevalence of normal and branched saturated fatty acids, their ratio (ranged from 0.92 to 7.13), and the absence of fungal marker 18:2ω6 fatty acid. The principal component analysis showed a strong negative impact of heavy metals Na and B on main microbial and PLFA profiles. In contrast, stock of main chemical parameters, including Ca, K, Fe, and pH, was positively correlated with the microbial community structure.

Response of Microbial Communities in Soil to Multi-Level Warming in a Highland Barley System of the Lhasa River

No studies have examined the effect of experimental warming on the microbial biomass and community composition of soil in agricultural ecosystem on the Qinghai-Tibet Plateau. Thus it is unclear whether the influences of experimental warming on microbial communities in soil are related to warming magnitude in croplands on this Plateau. This study performed warming experiment (control, low- and high-level) in a highland barley system of the Lhasa River in May 2014 to examine the correlation between the response of microbial communities in soil to warming and warming magnitude. Topsoil samples (0–10 and 10–20 cm) were collected on September 14, 2014. Experimental warming at both low and high levels significantly increased soil temperature by 1.02 °C and 1.59 °C, respectively at the depth of 15 cm. Phospho lipid fatty acid (PLFA) method was used to determine the microbial community in soil. The low-level experimental warming did not significantly affect the soil's total PLFA, fungi, bacteria, arbuscular mycorrhizal fungi (AMF), actinomycetes, gram-positive bacteria (G+), gram-negative bacteria (G–), protozoa, the ratio of fungi to bacteria (F/B ratio), and ratio of G+ to G– (G+/G– ratio) at the 0–10 and 10–20 cm depth. The low-level experimental warming also did not significantly alter the composition of microbial community in soil at the 0–10 and 10–20 cm depth. The high-level experimental warming significantly increased total PLFA by 74.4%, fungi by 78.0%, bacteria by 74.0%, AMF by 66.9%, actinomycetes by 81.4%, G+ by 67.0% and G– by 74.4% at the 0–10 cm depth rather than at 10–20 cm depth. The high-level experimental warming significantly altered microbial community composition in soil at the 0–10 cm depth rather than at 10-20 cm depth. Our findings suggest that the response of microbial communities in soil to warming varied with warming magnitudes in the highland barley system of the Lhasa River.

Change in straw decomposition rate and soil microbial community composition after straw addition in different long-term fertilization soils

Fertilization practices can change soil fertility and biological properties, and influence its ecological functions. We studied the change in the straw decomposition rate and microbial community composition in soils with different long-term fertilization regimes (no-fertilizer control (CK); nitrogen, phosphorus, and potassium fertilizers (NPK); and NPK plus straw (NPKS)) with addition of straw in a 75-day incubation experiment. Carbon dioxide (CO2) emission rates from the straw material were 13.9, 15.8, and 17.9 μg C g−1 soil day−1 in the CK + S, NPK + S, and NPKS + S treatments, respectively. After straw addition, the biomass of fungi and bacteria increase following the order of CK + S ≤ NPK + S < NPKS + S; while the bacterial richness decreased and did not change with incubation time, the fungal richness decreased and presented different responses among treatments with incubation time. Their diversities presented a decreasing-increasing trend with incubation time in all treatments. The richness and diversity of bacteria and fungi were positively correlated with soil NO3−–N. Bacterial community structure on days 1 and 3 were significantly separated from that on day 75; however, fungal community structure did not differ significantly as that of bacteria across different stages in the same treatment. A redundancy analysis showed that straw addition changed the community structure of bacteria and fungi by decreasing soil NO3−–N, and their community structures were regulated by soil organic C in the early stage and by NH4+–N in the later incubation stage. The relative abundance of the bacterial phyla Proteobacteria, Firmicutes, and fungal phyla Ascomycota showed synchronized changes with straw CO2 emissions rate. Our findings suggested that long-term fertilization and the return of straw to soils increased straw decomposition relative to the unfertilized soil, the latter difference in decomposition attributed to greater biomass of bacteria and fungi resulting from the improvement in soil fertility.

Microbial community biomass and structure in saline and non-saline soils associated with salt- and boron-tolerant poplar clones grown for the phytoremediation of selenium

ABSTRACTPoplar trees (Populus spp.) are often used in bioremediation strategies because of their ability to phytoextract potential toxic ions, e.g., selenium (Se) from poor quality soils. Soil microorganisms may play a vital role in sustaining health of soil and/or tolerance of these trees grown in poor quality soils by contributing to nutrient cycling, soil structure, overall soil quality, and plant survival. The effect of naturally occurring salts boron (B) and Se on soil microbial community composition associated with poplar trees is not known for bioremediation strategies. In this study, three Populus clones 13–366, 345–1, and 347–14 were grown in spring 2006 under highly saline, B, and Se clay-like soils in the west side of the San Joaquin Valley (SJV) of CA, as well as in non-saline sandy loam soils located in the east side of the SJV. After 7 years of growing in the respective soils of different qualities, soil samples were collected from poplar clones grown in saline and non-saline soils to examine and compare soil quality effects on soil microbial community biomass and composition. The phospholipid fatty acid (PLFA) analysis was used to characterize microbial community composition in soils from trees grown at both locations. This study showed that microbial biomass and the amount and proportion of arbuscular mycorrhizal fungal (AMF) community were lower in all three poplar clones grown in saline soil compared to non-saline soil. Amounts of Gram + bacterial and actinomycetes PLFAs were significantly lower in poplar clone 13–366 grown in saline soil compared to non-saline soil; however, they did not differ significantly in poplar clones 347–14 and 345–1. Additionally, amounts of saprophytic fungal, Gram − bacterial and eukaryotic PLFA remained similar at saline and non-saline sites under poplar clones 347–14, 345–1, and 13–366. Therefore, this study suggested that salinity and B do have an impact on microbial biomass and AMF; however, these poplar clones still recycled sufficient amount of nutrients to support and protect saprophytic fungal and bacterial communities from the effects of poor quality soils.

Key microbial taxa in the rhizosphere of sorghum and sunflower grown in crop rotation

Microbes are key determinants of plant health and productivity. Previous studies have characterized the rhizosphere microbiomes of numerous plant species, but little information is available on how rhizosphere microbial communities change over time under crop rotation systems. Here, we document microbial communities in the rhizosphere of sorghum and sunflower (at seedling, flowering and senescence stages) grown in crop rotation in four different soils under field conditions. A comprehensive 16S rRNA-based amplicon sequencing survey revealed that the differences in alpha-diversity between rhizosphere and bulk soils changed over time. Sorghum rhizosphere soil microbial diversity at flowering and senescence were more diverse than bulk soils, whereas the microbial diversity of sunflower rhizosphere soils at flowering were less diverse with respect to bulk soils. Sampling time was also important in explaining the variation in microbial community composition in soils grown with both crops. Temporal changes observed in the rhizosphere microbiome were both plant-driven and due to seasonal changes in the bulk soil biota. Several individual taxa were relatively more abundant in the rhizosphere and/or found to be important in maintaining rhizosphere microbial networks. Interestingly, some of these taxa showed similar patterns at different sampling times, suggesting that the same organisms may play the same functional/structural role at different plant growth stages and in different crops. Overall, we have identified prominent microbial taxa that might be used to develop microbiome-based strategies for improving the yield and productivity of sorghum and sunflower.

Soil anammox community structure in different land use soils treatment with 13C urea as determined by analysis of phospholipid fatty acids.

The anaerobic ammonium oxidation (anammox) process is globally an important nitrogen-cycling process mediated by specialized microbes. However, still little information is documented about anammox microbial community structure under agricultural soils. The anaerobic incubation experiment was conducted to study the impacts of different land use soils fertilized by 13C-urea on the activity and diversity of anammox bacteria using stable isotope to probe the phospholipid fatty acid (PLFA-SIP). The 13C was preferentially incorporated in ratios PLFAs 16:1ω7c, 16:1ω5c, and 16:0. The results revealed that the abundance of the anammox bacteria (both hzs-β and hzo) were observed in vegetable soil V1 and paddy soils (R1 and R2) means that they were positively correlated with 13C-urea but were negatively correlated with NO3--N and NH4+-N concentrations. Thus, 13C-PLFAs 16:1ω7c, 16:1ω5c, and 16:0 could be the biomarker as soil anammox. The anaerobic microbial community composition of soils under different land use systems was diverse, and V1, R1, and R2 had similar microbial diversity and higher microbial biomass. The principal component analysis between soil properties and gene abundance suggested that not only pH but also soil organic matter, available P, and available K were important factors for the anammox process. This study suggested that 13C-Urea-PLFA for anaerobic incubation was a simple method to study anammox microbial community structure through affecting the soil nutrients, and the different land use systems played important roles in determining the microbial composition of soils.

Comparison of fatty acid methyl ester methods for characterization of microbial communities in forest and arable soil: Phospholipid fraction (PLFA) versus total ester linked fatty acids (EL-FAME)

Phospholipid fatty acid (PLFA) and ester-linked fatty acid methyl ester (EL-FAME) extraction methods have been commonly used for estimating microbial biomass and characterizing microbial community composition in soil. However, to our knowledge, there is currently no comparison of these two methods across different ecosystems. A regression analysis for 8 different soils showed that there were significant linear relationships between PLFA and EL-FAME extracts (r2=0.97, 0.98 and 0.72, respectively) for determining the fungal (18:2ω6,9) and bacterial abundance and fungal-to-bacterial ratio (F:B ratio). However, regression lines of forest soils for fungal abundance and F:B ratio had a slight but significantly higher intercept than those of arable soils, i.e. higher EL-FAME:PLFA ratio for fungi in forests than those in arable soils. This might be due to that EL-FAME extracts may have additional factors such as physiological status of fungi and the inclusion of substantial amount of humic substances that affect quantitative determination of fungal biomass. Overall, EL-FAME method is simple and would produce similar results to PLFA method for bacteria in both quantitative and qualitative assessments when comparing different soils across ecosystems. However, for fungi, PLFA method would be more suitable than EL-FAME method.

Changes in land use driven by urbanization impact nitrogen cycling and the microbial community composition in soils

Transition of populations from rural to urban living causes landscape changes and alters the functionality of soil ecosystems. It is unclear how this urbanization disturbs the microbial ecology of soils and how the disruption influences nitrogen cycling. In this study, microbial communities in turfgrass-grown soils from urban and suburban areas around Xiamen City were compared to microbial communities in the soils from rural farmlands. The potential N2O emissions, potential denitrification activity, and abundances of denitrifiers were higher in the rural farmland soils compared with the turfgrass soils. Ammonia oxidizing archaea (AOA) were more abundant than ammonia oxidizing bacteria (AOB) in turfgrass soils. Within turfgrass soils, the potential nitrification activities and AOA abundances were higher in the urban than in the suburban soils. These results indicate a more pivotal role of AOA in nitrification, especially in urban soils. Microbial community composition was distinctly grouped along urbanization categories (urban, suburban, and rural) classified according to the population density, which can in part be attributed to the differences in soil properties. These observed changes could potentially have a broader impact on soil nutrient availability and greenhouse gas emissions.