Abundance Of Nitrospira Research Articles

Intra-horizon differentiation of the bacterial community and its co-occurrence network in a typical Plinthic horizon

Subsurface soil bacterial community composition and the controlling factors remain largely unknown, especially the micro-zone differentiation of community composition within a horizon. We studied a plinthic horizon to determine how different micro-zones in a horizon affect the bacterial community. The plinthic horizon is a net-like horizon characterized by the segregation of iron forms as shown by contrasting red matrix and white veins, which share common macro-environmental conditions such as climate and land use but differ only in physical and chemical compositions. The studied horizon is typical of the red soils of southeastern China and is an important layer in the red soil Critical Zone. The plinthite is considered to have been formed in the Quaternary and thus is a record of the paleo-environment. We evaluated the difference in the bacterial community composition between the red matrix and white veins and explored the possible assembly mechanisms of their co-occurrence patterns. Compared to the eutrophic environments of a red matrix, higher relative abundances of Acidobacteria and Nitrospirae were observed in the white veins. Similarly, more niches led to a higher density of bacterial co-occurrence patterns in the red matrix. The differences in the bacterial community composition and association networks are due to environmental selection, including the legacy of the paleoclimate that is represented by major element contents and contemporary hydrological properties that are mainly controlled by the soil texture. Our study shows that micro-zones even within a same plinthic horizon can provide different habitats and thus select for specific bacterial communities. Furthermore, this study could improve our understanding of the differentiation of bacterial communities among microenvironments caused by both historical and contemporary processes and help to predict how these communities may respond to future environmental changes.

Soil microbial community and carbon and nitrogen fractions responses to mulching under winter wheat

Mulching enhances soil C and N fractions compared to no mulching, but its impact on soil microbial communities and their relations to C and N fractions with mulching are not clear. We studied the 9-yr effect of no mulching (CK), straw mulching (SM), and plastic film mulching (PM) on soil bacterial and fungal community structure and their relationships to soil C and N fractions under dryland winter wheat in the Loess Plateau of China. The SM did not affect bacterial diversity and richness, but enhanced fungal diversity and richness compared to CK in subsoil layers. The PM also increased fungal diversity and richness, but reduced bacterial diversity and richness compared to SM and CK. Compared to CK, the relative abundance of Actinobacteria was lower with SM at 0–10 cm, but the abundances of Nitrospirae, Firmicutes, WS3, and Zygomycota were greater with PM at most soil depths. Bacterial diversity correlated with soil C and N fractions, and fungal richness with potential N mineralization and microbial biomass C and N. Although plastic film mulching enhanced fungal diversity and richness compared to no mulching, straw mulching was more effective in maintaining soil microbial diversity and richness and enhancing soil C and N fractions under dryland winter wheat.

Comammox Nitrospira are the dominant ammonia oxidizers in a mainstream low dissolved oxygen nitrification reactor

Recent findings show that a subset of bacteria affiliated with Nitrospira, a genus known for its importance in nitrite oxidation for biological nutrient removal applications, are capable of complete ammonia oxidation (comammox) to nitrate. Early reports suggested that they were absent or present in low abundance in most activated sludge processes, and thus likely functionally irrelevant. Here we show the accumulation of comammox Nitrospira in a nitrifying sequencing batch reactor operated at low dissolved oxygen (DO) concentrations. Actual mainstream wastewater was used as influent after primary settling and an upstream pre-treatment process for carbon and phosphorus removal. The ammonia removal rate was stable and exceeded that of the treatment plant's parallel full-scale high DO nitrifying activated sludge reactor. 16S rRNA gene sequencing showed a steady accumulation of Nitrospira to 53% total abundance and a decline in conventional ammonia oxidizing bacteria to <1% total abundance over 400 + days of operation. After ruling out other known ammonia oxidizers, qPCR confirmed the accumulation of comammox Nitrospira beginning around day 200, to eventually comprise 94% of all detected amoA and 4% of total bacteria by day 407. Quantitative fluorescence in-situ hybridization confirmed the increasing trend and high relative abundance of Nitrospira. These results demonstrate that comammox can be metabolically relevant to nitrogen transformation in wastewater treatment, and can even dominate the ammonia oxidizing community. Our results suggest that comammox may be an important functional group in energy efficient nitrification systems designed to operate at low DO levels.

Changes in the soil microbial community are associated with the occurrence of Panax quinquefolius L. root rot diseases

Root-rot disease, a catastrophic disease of Panax quinquefolium L. causes yield reduction and serious economic losses. However, knowledge of the relationship between rhizosphere microbial community and root-rot disease is limited. This study is aim to test whether the bacteria and fungi community differed between the soil attached to healthy and rotten roots of American ginseng. Moreover, the effects of American ginseng cultivation for 4 years on changes of soil physiochemical properties and microbial community were also investigated. High-throughput sequencing (Illumina MiSeq) was used to investigate the difference of microbial communities in the soils of new farmland (C) and the rhizosphere soils around healthy (H) and root rot diseased ginseng (R). Cultivation of American ginseng for 4 years not only changed the soil physicochemical properties, but also significantly increased the richness of the soil bacteria and decreased the fungal richness and diversity. Compared with other genera, the bacterial genera Nitrospira and the fungal genera Gibberella and Podospora were strongly enriched in the soil of new farmland. However, the relative abundance of Janthinobacterium, Nitrospira and Pedomicrobium in bacterial community, and Mrakia, Paradendryphiella, Sporopachydermia, Myrothecium and Racocetra in fungal community were significantly decreased after culture of American ginseng. The results also showed that the bacteria and fungi community differs between the soil attached to healthy and rotten roots of American ginseng. The richness indices of fungal community showed a significant decrease in rhizosphere soils of R comparing with H. The bacteria Rhodoplanes and Kaistobacter were the dominant genera in the H sample, whereas Sphingobium was dominant in the R sample. Notably, Monographella was significantly higher in the R sample (23.13%) than that of H sample (2.90%). In addition, the fungi Melanophyllum and Staphylotrichum were the most differently abundant in the H sample, whereas Mortierella and Cistella were the differently abundant genera in the R sample. Our results indicate that cultivation of American ginseng changed the edaphic factors and the soil microbial community, and there are significant differences in the microbial community between the soil attached to healthy and rotten roots of American ginseng.

Biochars reduced the bioaccessibility and (bio)uptake of organochlorine pesticides and changed the microbial community dynamics in agricultural soils

Biochar is considered as a universal sorbent used for soil amendment but its impacts on organochlorine pesticides (OCPs) and microbial communities associated with soil and vegetables are unclear. The effects of different biochars (derived from sewage sludge biochar (SSBC), soybean straw biochar (SBBC), rice straw biochar (RSBC) and peanut shells biochar (PNBC)), on bioaccessible fractions of OCPs in a contaminated soil and their subsequent bioaccumulation into vegetables (Chinese cabbage and spring onion) were investigated in this research work. The influence of these amendments on vegetable yields and soil microbial community using Illumina next generation sequencing technology was also assessed. The application of selected biochars significantly (p < 0.01) reduced the bioaccessibility of ∑OCPs in contaminated soil: SSBC (52%), PNBC (51%), RSBC (60%), and SBBC (47%), as compared to the control. The results indicated that following biochar additions, the bio-uptake of ∑OCP bio-uptake was considerably (from 86 to 85%) reduced in grown vegetables. Risk assessment showed that biochar amendments markedly (p < 0.01) decreased the hazard quotient (HQ) indices and incremental lifetime cancer risk (ILTR) values for OCPs associated with the consumption of vegetables. In addition, the results of high-throughput sequencing showed significant differences in microbial community structure between the treatments, which was driven by differences in the relative abundances of soil microbes. The relative abundances of Acidobacteria, Chloroflexi, Nitrospirae and Verrucomicrobia decreased following biochar additions. However, biochar amendments increased the relative abundances of Actinobacteria, Proteobacteria, Planctomycetes, Bacteroidetes, Firmicutes, and Gemmatimonadetes, though the increase in relative abundances of these phyla was strongly dependent on the type of biochar used.

Characteristics of the sludge filterability and microbial composition in PAC hybrid MBR: Effect of PAC replenishment ratio

Periodic withdrawal and replenishment of powdered activated carbon (PAC) hybrid membrane bioreactor (MBR) is required for stable performance. The influence of the replenishment of powdered activated carbon (PAC) on sludge filterability and microbial community in hybrid MBRs was investigated. Results showed that the removal of organic matter and nitrogen were not significantly affected by the PAC refreshment, while soluble microbial products (SMP) concentration decreased and extracellular polymeric substance (EPS) increased with increasing PAC replacement ratio. MBR system with PAC replenishment exhibited low fouling propensity and prolonged filtration agreed well with fouling rate and resistance analysis. Molecular weight distribution of SMP in MBR confirmed the synergistic effects of PAC adsorption/biodegradation and membrane interception on organics removal. Microbial activity was positive associated with the PAC replenishment ratio. Moreover, the high-throughput sequencing indicated that due to fresh PAC added, the increased abundance of Proteobacteria, Bacteroidetes and Nitrospira guaranteed the pollutant removal, and the membrane fouling caused by Planctomycetes and Betaproteobacteria decreased. An optimal PAC replenishment ratio at 1.67% achieved the effective membrane fouling mitigation and enhanced dominant bacterial structure. PAC refreshment is considered to be a promising way to advance the application of MBR.

Effect of biogas slurry addition on soil properties, yields, and bacterial composition in the rice-rape rotation ecosystem over 3 years

Organic treatments may improve soil nutrient availability and ecological functions. This study aimed to determine the effect of biogas slurry (BS) on soil properties, yields, and bacterial community activity and to examine the main environmental factors impacting bacterial compositions in the ecosystem. A 3-year field experiment was conducted in yellow soil under a rice-rape rotation to understand the effect of BS originating from anaerobically digested pig waste on soil chemical and bacterial compositions. Compared with an inorganic nutrient treatment and a control, adding BS at a moderate dose (BS6, 165.1 t ha−1) positively affected the rice and rape yields, soil fertility, and bacterial diversity. The BS was more suitable than chemical fertilizer for maintaining agricultural soil sustainability, especially the BS6 and BS7 treatments (165.1 and 182.1 t ha−1, respectively), by improving nutrient content, increasing soil pH, and promoting soil crumb structure formation. The relative abundance of Actinobacteria in BS6 was decreased by 37.9% compared with the untreated soil and 27.7% compared with the fertilizer treatment, while the relative abundance of Nitrospirae in BS6 increased by 41.2% and 43.5% compared with these treatments, respectively. Redundancy analyses (RDA) showed that pH, rape yield, cation exchange capacity (CEC), and total nitrogen (TN) were significantly correlated with soil bacterial community composition and explained 56.0%, 46.4%, 43.2%, and 34.9% of the total community variability, respectively. The soil bacterial diversity depended mainly on soil pH, and crop rotation played an important role in changing the bacterial community. The soil bacterial composition was clearly altered after 3 years of BS treatments. These increases in bacterial diversity could be of ecological significance in maintaining soil fertility and functionality.

Performance of physical and chemical methods in the co-reduction of internal phosphorus and nitrogen loading from the sediment of a black odorous river

The continuous release of nutrients from sediment is a major barrier to the remediation of black odorous rivers. This study used a long-term laboratory incubation experiment to investigate the effectiveness of sediment dredging, intermittent aeration, and in situ inactivation with modified clays to reduce the internal loading of sediment from a seriously polluted river. The results indicated that intermittent aeration and in situ inactivation were effective in reducing the TN and NH4+ concentrations in the water column. However, sediment dredging did not consistently reduce the TN and NH4+ concentrations in the water column. In contrast, the three methods were all effective in controlling the TP and PO43− concentrations in the water column. Except for dredging, >30% of NH4+ and 40% of PO43− fluxes from sediment were reduced when compared with a control sample after 120 days of remediation. Dredging induced a significant release of NH4+ from sediment. Dredging and aeration made nearly no change to the amount of extractable nitrogen in the sediment. However, inactivation may increase sediment-extractable ammonium in deep sediment layers with time due to vertical transportation of clay by intensive bioturbation. Dredging is the most effective way to reduce surface mobile phosphorus over time while the transported clays can reduce a large percentage of the mobile phosphorus in deeper sediment. The relative abundance of Nitrospira in the surface sediment increased significantly with each remediation measure, creating favorable conditions for the reduction of the ammonium released from sediment. Altogether, the results of this study indicated that clay inactivation is the best method for controlling the internal loading of both phosphorus and nitrogen in seriously polluted river sediment.

Impact of free nitrous acid shock and dissolved oxygen limitation on nitritation maintenance and nitrous oxide emission in a membrane bioreactor

This study investigated the initiation and maintenance of nitritation in a membrane bioreactor (MBR) with long solids retention time (SRT) of 43.8 days. Nitritation was initiated within 65 days in the MBR via dissolved oxygen (DO) limitation (<0.5 mg/L). However, nitrite oxidizing bacteria (NOB) (Nitrospira and Nitrobacter) acclimated to the low DO environment and proliferated from day 81, leading to nitrate accumulation. Thereafter, the combined strategy of DO limitation and in-situ generated free nitrous acid (FNA) shock successfully restored and maintained stable nitritation for >70 days. Quantitative polymerase chain reaction (qPCR) results showed that cell abundances of Nitrospira and Nitrobacter decreased by between 50.0 to 68.9% and 60.6 to 96.4%, respectively following the FNA shocks. The maximum ammonium loading rate achieved was 1.81 kg N/(m3 day) with ammonium removal ratio and nitrite accumulation ratio of over 0.97 and 0.96, respectively. Average emission rate of N2O from the MBR was 2.1 ± 0.72% of ammonium removed. FNA shock on day 195 reduced the N2O emission by 13.6%. The strategy developed in this study verified that spiked FNA shock together with DO limitation can be used for maintaining nitritation in MBRs with long SRTs. This method can potentially allow for maintaining nitritation at relatively low capital and operating expenditure when treating high concentration ammonium wastewater.

Crop diversity facilitates soil aggregation in relation to soil microbial community composition driven by intercropping

Studies verify that intercropping increases soil macro-aggregates but the mechanism underlying the increase is poorly understood. Three long-term field experiments were conducted starting in 2009 at three sites in an oasis in northwest China. The first was a split-plot design: Rhizobium (with or without inoculation) and three cropping systems (faba bean/maize intercropping and corresponding monocultures). The second and third experiments were both single-factorial randomized block designs with nine cropping systems (maize intercropped with faba bean, chickpea, soybean, or oilseed rape, and the corresponding monocultures). Soil aggregates were determined by the wet sieving method. Microbial biomass and community composition in 2015 and 2016 were determined by phospholipid fatty acid (PLFA) and high throughput sequencing analysis of 16S rRNA. Soil macro-aggregates (> 2 mm) in intercropping systems increased by 15.5–58.6% across three sites and two years, an effect derived partly from increased relative abundance of soil Sordariales, from enhanced arbuscular mycorrhizal fungi biomass, or from reduced relative abundance of Nitrospirae, depending on soil type. Intercropping alters soil microbial community composition and further facilitates soil aggregation. These findings provide insights into the mechanisms underlying the maintenance of biodiversity in ecosystem functioning.

Dynamics of Bacterial Communities in a 30-Year Fertilized Paddy Field under Different Organic–Inorganic Fertilization Strategies

Fertilization plays important roles in improving soil fertility and in increasing crop yield. Soil microbial communities are sensitive indicators of soil quality and health, which could be affected by fertilization strategy. However, our knowledge on how organic–inorganic fertilizers application affects soil bacterial communities remains largely poorly understood. In this study, we investigated the long-term effects of different organic–inorganic fertilization strategies: without fertilizer (CK), fertilizers NPK (CF), fertilizers NPK, plus 30% organic manure (CFM1), and fertilizers NPK plus 60% organic manure (CFM2) on soil bacterial communities in paddy fields. Results showed that the bacterial 16S ribosomal DNA (rDNA) gene abundances in treatments CF, CFM1, and CFM2 were 1.44, 1.54, and 1.28 times higher than that in CK and the ACE index in treatment CFM1 was 9.0% greater than that in treatment CFM2, respectively. Fertilization strategy significantly changed the relative abundance of Nitrospirae, Gemmatimonadetes, and unclassified bacteria at the phylum level and bacteria belonging to order Nitrospira, candidate bacterium SBR2076, unclassified bacteria, Syntrophobacterales, and Solibacterales at the order level, respectively. High organic–inorganic fertilizer application rates inhibited the growth of Nitrospirae by 20–35%, and stimulated the growth of Gemmatimonadetes by 14–77%, relative to the rest of the treatments, respectively. Hierarchical cluster and principal coordinate analysis (PCoA) showed that the fertilization strategy affected the bacterial community structures, and the organic–inorganic fertilized treatments possessed similar bacterial community structures. Furthermore, soil pH, total nitrogen (TN), and soil organic carbon (SOC) were the main driving factors altering the bacterial communities. Our results suggested that combined organic–inorganic fertilizers application increased soil nutrient contents and bacterial abundances, and this could be an optimized fertilization strategy in regulating soil bacterial communities for rice production.

Effect of exogenous nitrogen and phosphorus inputs on the microbe-soil interaction in the secondary Castanopsis sclerophylla forest in east China

Abstract: Soil microbes play a key role in the formation and decomposition of organic materials and in the improvement of the ecological environment. Despite continuous increases in nitrogen (N) and phosphorus (P) inputs due to the atmospheric deposition or fertilization, the response of soil to exogenous inorganic nutrients inputs remains elusive. By a manipulative experiment we simulated N and P depositions in a subtropical secondary Castanopsis sclerophylla forest in east China over the period 2011-2015, to evaluate the impact of inorganic nutrient addition on soil bacterial communities. Four treatments were administered (control and nutrient-enrichment: N, P, and N+P), with N added at a total of 100 kg N ha-1 yr-1 in the form of NH4NO3, and P at 50 kg P ha-1 yr-1 in Ca(H2PO4)2, sprayed near the soil surface at the end of each trimester. Quantitative PCR technique and Illumina platform-based sequencing analysis of the V3-V4 16S rRNA gene region were performed on total DNA extracted from soil samples to characterize the soil bacterial community abundance and diversity. As Proteobacteria, Acidobacteria and Actinobacteria were the predominant phyla in all conditions, treatments did not alter the distribution of bacterial phyla, while their relative abundances responded differently to N, P additions. A GLMM analysis showed that N input significantly (P < 0.05) reduced the relative abundance of Acidobacteria (13.11%), Bacteroidetes (0.6%), Elusimicrobia (0.21%), Nitrospirae (0.1%) and TM6 (0.04%). Relative abundance after P treatment significantly (P < 0.01) decreased for Nitrospirae (0.07%), and pronounced interactive effects of N and P additions (N:P) were observed on phylum Nitrospirae (P < 0.01) and TM6 (P < 0.05). Moreover, redundancy analysis revealed that soil pH was closely related to the bacterial community (r2 = 0.622, P = 0.015). Our findings suggest that exogenous N and P inputs affected the relative abundances and caused compositional shifts in the local bacterial community that closely associated with soil pH, thus providing the evidence that microbe-soil interactions are influenced by N and P availability in subtropical forest ecosystem of east China.

High-rate partial nitrification of semiconductor wastewater: Implications of online monitoring and microbial community structure

The aims of this study were to investigate the feasibility of partial nitrification (PN) in a sequencing batch reactor (SBR) fed with real wastewater discharged from the washing process at a semiconductor factory, to evaluate the efficacy of online control for nitrite buildup, and to examine the microbial community composition. To this end, online monitoring of NH4+ and NO3− concentrations in an SBR was implemented to track the extant activities of ammonia-oxidizing (AOB) and nitrite-oxidizing bacteria (NOB). The results showed that the rate of NH4+ oxidation by AOB increased during the first 20 days of the operation, and were maintained as high as a maximum volumetric rate of NH4+ removal of 2.17 kg-N/m3/day with an NH4+ removal efficiency of 94.1–99.8%. Successful nitrite buildup (> 99.9%) has been achieved after day 20 when AOB activity was 8.11-times higher than NOB activity. High-throughput sequencing of 16S rRNA genes manifested that the relative abundance of cluster 7 Nitrosomonas species in the family Nitrosomonadaceae increased from 0.2% to 50% over total bacteria. On the other hand, the relative abundance of Nitrospira spp. as the predominant NOB decreased from 1.0% to 0.05%, indicating NOB out-selection during SBR operations. A positive correlation was noted between the abundance of the dominant AOB and NH4+ oxidation rate, suggesting that a simple nitrifier community regulated high-rate PN.

Transcriptional activity and diversity of comammox bacteria as a previously overlooked ammonia oxidizing prokaryote in full-scale wastewater treatment plants

The discovery of complete ammonia oxidizing bacteria (CAOB) has fundamentally overturned the traditional recognition of nitrification. However, little was known about the transcriptional activity and diversity of the newly recognized ammonia oxidizing prokaryote in engineered ecosystems. To fill this gap, transcriptional investigations of CAOB amoA genes were carried out comparatively with the canonical ammonia oxidizing bacteria (AOB) and archaea (AOA) in eight full-scale wastewater treatment plants (WWTPs). Remarkably, qPCR results revealed the transcriptional levels of CAOB amoA gene were unexpectedly high in most of samples with the highest 24-fold that of AOB amoA, suggesting CAOB were actively participating in ammonia oxidation while they were previously overlooked. This result also well explained the confusing high abundances of genus Nitrospira which were frequently detected in WWTPs. Furthermore, phylogenetic analysis based on high throughput sequencing indicated the CAOB amoA gene sequences formed three well-supported clusters and Nitrospira nitrosa cluster accounted for 97% of all the retrieved sequences, which was supposed to be the dominant taxon of CAOB in the ammonia-intensive environment due to niche partitioning. This study highlighted the significance of including the newly discovered ammonia oxidizing bacterial member when assessing the nitrification process and ecological function in the future.

Alterations in soil bacterial community in relation to Spartina alterniflora Loisel. invasion chronosequence in the eastern Chinese coastal wetlands

In order to better understand the variations in soil bacterial community and associated drivers following plant invasion, we investigated changes in soil bacterial community along with 9-, 13-, 20- and 23-year-old Spartina alterniflora Loisel. (SA) invasion in comparison with bare flat (BF) in the eastern Chinese coastal wetlands, based on analyses of quantitative polymerase chain reaction (qPCR) and Illumina MiSeq DNA sequencing of 16S rRNA gene. The SA invasion significantly elevated soil bacterial abundance and diversity relative to BF, with the highest levels in 9-year-old SA soil, which gradually decreased with SA invasion from 9 to 23 years. The abundance of copiotrophic Proteobacteria, β-proteobacteria, and Bacteroidetes generally diminished along with SA invasion chronosequence. While, changes in abundance of oligotrophic Chloroflexi, Acidobacteria, Nitrospirae and Planctomycetes exhibited opposite trends. Our data suggest that soil nutrient substrates, and physiochemical properties (soil pH and/or moisture) primarily drive the shifts in soil bacterial abundance, diversity, and community composition along with SA invasion chronosequence in the costal wetlands of eastern China. Overall, soil bacterial abundance and diversity peaked in 9-year-old SA community, with soil bacterial community composition changing from copiotrophic to oligotrophic groups along with SA invasion chronosequence.

Changes in the Microbial Community Structure and Soil Chemical Properties of Vertisols Under Different Cropping Systems in Northern China

The cropping system changes the soil physical and chemical properties and directly influences the microbiome composition and diversity. Microflora are important drivers of the nutrient cycling process and can affect soil fertility, plant productivity and environmental sustainability. Here, the soil fertility and microbial community changes in four soybean-containing plant systems were studied for 12 years. Amplification sub-sequencing techniques were used to assess the differences in the soil community structure under different cropping systems and identified significant positive and negative fertility factors. The lowest effective P, Cu and Mn contents were obtained with the fallow-soybean planting mode. The soybean continuous cropping pattern yielded significantly increased effective organic matter (OM), significantly higher N, K, Mn and Fe contents and a lower effective P content. The wheat-soybean rotation cropping pattern produced the highest effective P and Cu contents and significantly lower OM and effective N and Fe contents, whereas the corn-soybean rotation planting system yielded the highest pH and significantly lower K and Zn contents (P<0.05). Different cropping systems yielded microbial communities with significant differences in diversity and relative abundances. Significantly higher microbial diversity was observed with the fallow-soybean planting mode, which showed significantly higher relative abundances of Chloroflexi, Verrucomicrobia, Nitrospirae and Bacteroidetes and a significantly lower relative abundance of Actinobacteria. The soybean continuous cropping pattern yielded significantly higher relative abundances of Proteobacteria, Bacteroidetes, and Actinobacteria and significantly lower relative abundances of Acidobacteria and Planctomycetes, whereas the wheat-soybean rotation cropping pattern generated significantly higher relative abundances of Planctomycetes, Gemmatimonadetes, candidate division WPS-1 and Armatimonadetes compared with the other planting systems. The fungi in all the samples were mainly distributed in Ascomycota, Basidiomycota and Zygomycota, and these groups reached relative abundances as high as 90%. The wheat-soybean rotation cropping pattern produced a significantly higher relative abundance of Ascomycota, and the fallow-soybean planting mode yielded a significantly higher relative abundance of Zygomycota. An extremely low soil fertility index greatly affects the microbial community structure, and the effective P, Cu, Mn, and K contents of black soil are environmental factors closely related to microbial diversity. These findings are of great significance for protecting the ecological environment.

Geospatial variation in co-occurrence networks of nitrifying microbial guilds.

Microbial communities transform nitrogen (N) compounds, thereby regulating the availability of N in soil. The N cycle is defined by interacting microbial functional groups, as inorganic N‐products formed in one process are the substrate in one or several other processes. The nitrification pathway is often a two‐step process in which bacterial or archaeal communities oxidize ammonia to nitrite, and bacterial communities further oxidize nitrite to nitrate. Little is known about the significance of interactions between ammonia‐oxidizing bacteria (AOB) and archaea (AOA) and nitrite‐oxidizing bacterial communities (NOB) in determining the spatial variation of overall nitrifier community structure. We hypothesize that nonrandom associations exist between different AO and NOB lineages that, along with edaphic factors, shape field‐scale spatial patterns of nitrifying communities. To address this, we sequenced and quantified the abundance of AOA, AOB, and Nitrospira and Nitrobacter NOB communities across a 44‐hectare site with agricultural fields. The abundance of Nitrobacter communities was significantly associated only with AOB abundance, while that of Nitrospira was correlated to AOA. Network analysis and geostatistical modelling revealed distinct modules of co‐occurring AO and NOB groups occupying disparate areas, with each module dominated by different lineages and associated with different edaphic factors. Local communities were characterized by a high proportion of module‐connecting versus module‐hub nodes, indicating that nitrifier assemblages in these soils are shaped by fluctuating conditions. Overall, our results demonstrate the utility of network analysis in accounting for potential biotic interactions that define the niche space of nitrifying communities at scales compatible to soil management.

Changes of the organic carbon content and stability of soil aggregates affected by soil bacterial community after afforestation

Soil aggregation is one of the most important factors affecting soil organic carbon (SOC) stabilization, and the stability of aggregates depends in part on soil microbial diversity and composition. Interactions between the soil bacterial community and SOC content in soil aggregates after afforestation are poorly understood. In this study, we investigated difference in the diversity of soil bacterial with high-throughput 16S rRNA sequencing, as well as the SOC content in soil aggregates representing a chronosequence of 42, 27, and 17 years of Robinia pseudoacacia L. succession (RP42, RP27, and RP17), and in farmland (FL) soil for comparison (millet (Setaria italica) and soybean (Glycine max) rotation).The SOC content in RP17, RP27, and RP42 plots were significantly higher than that of FL by an average of 85.57%, 142.37%, and 76.69% in large macro-aggregates (>1 mm), small macro-aggregates (0.25–1 mm), and micro-aggregates (<0.25 mm), respectively. The Simpson index for the FL plot was significantly higher than that of the RP17, RP27, and RP42 plots, whereas the Shannon index followed the opposite trend. The dominant bacterial phyla detected were Proteobacteria, Acidobacteria, and Actinobacteria in each afforested and FL sites. These data revealed significant correlations between soil aggregate characteristics, such as SOC content, mean weight diameter (MWD), and geometric mean diameter (GMD), with the relative abundance of Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae, Verrucomicrobia, and Planctomycetes. These relationships suggested that the effects of afforestation on SOC stabilization in soil aggregates are modulated by both soil aggregate size and also soil bacterial diversity. We demonstrate that the interaction between soil aggregate size and soil microbes might be a key factor in effective soil conservation, restoration, sustainability of agroecosystems, and erosion prevention.

Dietary l-arginine Supplementation Alleviates the Intestinal Injury and Modulates the Gut Microbiota in Broiler Chickens Challenged by Clostridium perfringens.

Our previous reports suggested that Dietary l-arginine supplementation attenuated gut injury of broiler chickens infected with Clostridium perfringens by enhancing intestinal immune responses, absorption and barrier function, but its effect on the gut microbiome of broiler chickens remains unclear. This experiment aimed at evaluating the effects of Dietary l-arginine supplementation on the gut bacterial community composition and function of broiler chickens challenged with C. perfringens. In total, 105 1-day-old male Arbor Acres broiler chickens were assigned to three groups: Control (CTL), C. perfringens-challenged (CP), and C. perfringens-challenged and fed diet supplemented with 0.3% l-arginine (ARGCP) groups. The challenge led to macroscopic and histomorphological gut lesions, decreased villus height and increased the number of Observed species, Shannon, Chao1 and ACE indices of ileal microbiota, whereas l-arginine addition reversed these changes. Moreover, the three treatments harbored distinct microbial communities (ANOSIM, P < 0.05). At the genus level, 24 taxa (e.g., Nitrosomonas spp., Coxiella spp., Ruegeria spp., and Thauera spp.) were significantly more abundant in CP group than in CTL group (P < 0.05), whereas the levels of 23 genera of them were significantly decreased by l-arginine supplementation (P < 0.05). The abundances of only 3 genera were different between CTL and ARGCP groups (P < 0.05). At the species level, the challenge promoted the relative abundance of Nitrospira sp. enrichment culture clone M1-9, Bradyrhizobium elkanii, Nitrospira bacterium SG8-3, and Pseudomonas veronii, which was reversed by l-arginine supplementation (P < 0.05). Furthermore, the challenge decreased the levels of Lactobacillus gasseri (P < 0.05). Predictive functional profiling of microbial communities by PICRUSt showed that compared with CP group, ARGCP group had enriched pathways relating to membrane transport, replication and repair, translation and nucleotide metabolism and suppressed functions corresponding to amino acid and lipid metabolisms (P < 0.05). The relative abundances of KEGG pathways in l-arginine-fed broilers were almost equal to those of the controls. In conclusion, l-arginine alleviated the gut injury and normalized the ileal microbiota of C. perfringens-challenged chickens to resemble that of unchallenged controls in terms of microbial composition and functionality.

Linking soil bacterial and fungal communities to vegetation succession following agricultural abandonment

Globally, the rate and extent of cropland abandonment increase greatly since 1950s. Knowledge of soil bacteria and fungi succession during long-term vegetation development is particularly limited for the abandoned croplands. In order to test the effects of agricultural abandonment on soil biota succession, we studied the soil bacterial and fungal composition and diversity in abandoned farmlands across a century of secondary vegetation successional gradient in China’s Qinling Mountains. Using high-throughput sequencing technologies, the soil fungal and bacterial communities were studied in 22 abandoned farmlands, as well as 7 adjacent arable fields representing non-abandoned references. The stand age, i.e., years since agricultural abandonment, affected the soil bacterial and fungal composition and explained 8.7 and 31.6% variations of bacterial and fungal communities (at order level), repectively. The Proteobacteria, dominated by chemoorganotrophic bacteria, kept its absolute dominance status (38.66% - 40.77%) constantly during succession even though the vegetation changed obviously from crop to grass, shrub, and forest. The relative abundances of Acidobacteria, Planctomycetes, Verrucomicrobia, Nitrospirae, and Spirochaetes increased significantly with stand age (i.e., years since abandonment), while the Firmicutes, Actinobacteria, Gemmatimonadetes, Cyanobacteria, and Armatimonadetes showed an opposite trend. A distinct shift in fungal communities from Ascomycota -dominant in young stands to Basidiomycota -dominant in older stands was observed, which could be attributed to the increase of vegetation coverage and soil moisture during succession. The soil bacterial richness and diversity increased logarithmically with increasing stand age and gradually reached equilibrium in late-successional stage. Soil fungal diversity tended to increase in the early successional stages and then followed by a decreasing trend. The soil pH was the most important environmental factor predicating the soil fungal α-diversity measurements. Both the soil bacterial and fungal communities displayed successional trends along with vegetation succession. The soil bacteria and fungi exhibited marked differences in successional pattern during secondary succession following agricultural abandonment.