Development of microbial community structure in vegetable-growing soils from open-field to plastic-greenhouse cultivation based on the PLFA analysis

Purpose

The objectives of this study were to investigate (i) how the changes in cultivation pattern of vegetable affect soil microbial communities and (ii) the relationships between soil physico-chemical properties and microbial community structure.

Materials and methods

Soil samples were collected from fields growing vegetable crops with various times of plastic-greenhouse cultivation (0, 1, 4, 7 and 15 years, respectively). Phospholipid fatty acid (PLFA) analysis was conducted to reveal the soil microbial community of the test soils.

Results and discussion

The open-field soil had the highest total PLFAs amount. Although the Shannon-Weaver index was also highest in the open-field soil, the difference was not significant. Plastic-greenhouse cultivation decreased PLFAs species diversity and richness. Cluster analysis and principal component analysis (PCA) of the PLFA profiles revealed distinct groupings at different times during plastic-greenhouse cultivation.

Conclusions

Ultimately, PLFA analyses showed that long-term plastic-greenhouse cultivation make the physiological status of soil microbial community worse and increased stress level of microorganisms. And soil microbial community was significantly affected by field water capacity and water-soluble organic carbon. The study highlights the potential risk of long-term plastic-greenhouse cultivation to soil microbial community.

     

Soil microbial abundance and community structure vary with altitude and season in the coniferous forests,China

Purpose

Soil microbes control the bioelement cycles and energy transformation in forest ecosystems, and are sensitive to environmental change. As yet, the effects of altitude and season on soil microbes remain unknown. A 560 m vertical transitional zone was selected along an altitude gradient from 3023, 3298 and 3582 m, to determine the potential effects of seasonal freeze-thaw on soil microbial community.

Materials and methods

Soil samples were collected from the three elevations in the growing season (GS), onset of freezing period (FP), deeply frozen period (FPD), thawing period (TP), and later thawing period (TPL), respectively. Real-time qPCR and polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) were used to measure the abundance and structure of soil microbial community.

Results and discussion

The bacterial, archaeal, and fungal ribosomal DNA (rDNA) copy numbers decreased from GS to freezing stage (FP and FPD) and then increased in thawing stage (TP and TPL). Similarly, the diversity of microbial community varied with seasonal freeze-thaw processes. The diversity index (H) of the bacterial and archaeal communities decreased from GS to FP and then increased to TPL. The fungal community H index increased in the freezing process.

Conclusions

Our results suggested that abundance and structure of soil microbial community in the Tibetan coniferous forests varied by season and bacterial and archaeal communities respond more promptly to seasonal freeze-thaw processes relative to fungal community. This may have important implications for carbon and nutrient cycles in alpine forest ecosystems. Accordingly, future warming-induced changes in seasonal freeze-thaw patterns would affect soil nutrient cycles via altering soil microbial properties.

     

Impacts of continuous excessive fertilization on soil potential nitrification activity and nitrifying microbial community dynamics in greenhouse system

Purpose

Sampling and analysis of greenhouse soils were conducted in Shouguang, China, to study continuous excessive fertilization effect on nitrifying microbial community dynamics in greenhouse environment.

Materials and methods

Potential nitrification activity (PNA), abundance, and structure of nitrifying microbial communities as well as the correlations with soil properties were investigated.

Results and discussion

Short-term excessive fertilization increased soil nutrient contents and the diversity of nitrifying microbial communities under greenhouse cultivation. However, the abundance and diversity of nitrifying communities decreased greatly due to the increase of soil acidity and salinity after 14 years of high fertilization in greenhouse. There was a significant positive correlation between soil PNA and the abundance of ammonia-oxidizing bacteria (AOB) but not that of ammonia-oxidizing archaea (AOA) in topsoil (0–20 cm) when pH ≥7. Soil PNA and AOB were strongly influenced by soil pH. The groups of Nitrososphaeraceae, Nitrosomonadaceae, and Nitrospiraceae were predominant in the AOA, AOB, and nitrite-oxidizing bacteria (NOB) communities, respectively. Nitrifying community structure was significantly correlated with soil electrical salinity (EC), organic carbon (OC), and nitrate nitrogen (NO₃ ^?–N) content by redundancy analysis (RDA).

Conclusions

Nitrification was predominated by AOB in greenhouse topsoil with high fertilizer loads. Soil salinity, OC, NO₃ ^?–N content, and pH affected by continuous excessive fertilization were the major edaphic factors in shaping nitrifying community structure in greenhouse soils.

     

Temporal dynamics of fungal communities in soybean rhizosphere

Purpose

Many biotic and abiotic factors influence the structural and functional diversity of microbial communities in the rhizosphere. This study aimed to understand the dynamics of fungal community in the soybean rhizosphere during soybean growth and directly compare the influence of abiotic and biotic factors in shaping the fungal communities across different growth periods.

Materials and methods

High-throughput sequencing based on internal transcribed spacer (ITS) region, quantitative PCR, and statistical analysis approaches were used to measure the fungal community structure, abundance, and dynamic changes of 63 rhizosphere soil samples which were taken from different fertilization regimes and rhizobium inoculation treatments during three soybean growth stages.

Results and discussion

Among the taxa examined, more than 16 fungal classes were detected from the 21 soil samples. Sordariomycetes was the most abundant class, followed by Dothideomycetes, Agaricomycetes, and Eurotiomycetes. Soybean growth stage was the most important factor determining the diversity patterns of the fungal communities. Fungal community diversity was closely related to the base-fertilizer application, and fungal community richness was associated with rhizobium inoculation. Beta diversity of the fungal community based on the Bray-Curtis distance was significantly related to plant growth stage. Network analysis showed that mutual cooperation among fungal taxa became more intimate during the plant growth.

Conclusions

Compared with edaphic properties, plant growth stage was the dominant factor in determining soil fungal community dynamics. Base-fertilizer and rhizobium inoculation affected the alpha diversity of the soil fungi.

     

Land use affects soil organic carbon of paddy soils: empirical evidence from 6280 years BP to present

Purpose

Submerged rice cultivation has been practiced in China for 7000 years. Empirical evidence on changes of soil organic carbon (SOC) contents in paddy soils over this historical time period is scarce. Therefore, a field study was conducted to investigate the effect of submerged rice cultivation on the accumulation and preservation of SOC in paddies.

Materials and methods

Two buried ancient paddy profiles (6280 years BP, named P-01 and P-03) in the Yangtze Delta of eastern China were excavated to illustrate the development of SOC contents in soils during the evolution of paddies under anthropogenic land use and environmental changes from the prehistoric period to the present time. Trends in SOC concentrations, total nitrogen concentrations, and stable carbon isotope ratio were identified for different points in time.

Results and discussion

Accumulation of organic carbon was found in the paddy soil layers of P-01 at 100–174 cm depth. This site was taken under submerged rice cultivation in about 6280 years BP. The average SOC concentration in the prehistoric paddy topsoil in 100–130 cm depth was 1.27 %, which is seven times higher than that in the adjacent uncultivated land at 103–130 cm depth of P-03. This implies that the paddy soil has experienced substantial CO₂ sequestration under submerged management during that time. By about 3320 years BP, organic carbon contents were halved, potentially due to marine inundation by sea level rise. Up to the year 2003, the SOC contents in all horizons in the present time paddy soil have increased, especially in the surface layer, indicative of continuous rice cultivation. However, due to rapid urbanization and industrialization, the cultivation of paddies in eastern China has gradually been discontinued leading to the loss of SOC stocks of approximately 10 % in a 6-year interval (from 2003 to 2009). A significant relationship between SOC and rice phytolith contents was found in the paddy soil horizons of P-01 (r?=?0.71, p?<?0.01) and P-03 (r?=?0.72, p?<?0.01), suggesting that phytolith-occluded organic carbon could be used as a biomarker to ascertain the development of SOC in the evolution of rice paddies over the past 6000 years.

Conclusions

Submerged rice cultivation led to a noticeable accumulation of SOC in paddies. Phytolith-occluded organic carbon could be used as a biomarker to monitor changes of OC contents in paddy soils.

     

Straw amendment to paddy soil stimulates denitrification but biochar amendment promotes anaerobic ammonia oxidation

Purpose

Organic matter amendment is usually used to improve soil physicochemical properties and to sequester carbon for counteracting climate change. There is no doubt that such amendment will change microbial activity and soil nitrogen transformation processes. However, the effects of straw and biochar amendment on anammox and denitrification activity and on community structure in paddy soil are unclear.

Materials and methods

We conducted a 30-day pot experiment using rice straw and rice straw biochar to deepen our understanding about the activity, microbial abundance, and community structure associated with soil nitrogen cycling during rice growth.

Results and discussion

Regarding activity, anammox contributed 3.1–8.1% of N₂ production and denitrification contributed 91.9–96.9% of N₂ production; straw amendment resulted in the highest denitrification rate (38.9 nmol N g^?1 h^?1), while biochar amendment resulted in the highest anammox rate (1.60 nmol N g^?1 h^?1). Both straw and biochar amendments significantly increased the hzsB and nosZ gene abundance (p < 0.05). Straw amendment showed the highest nosZ gene abundance, while biochar amendment showed the highest hzsB gene abundance. Phylogenetic analysis of the anammox bacteria 16S rRNA genes indicated that Candidatus Brocadia and Kuenenia were the dominant genera detected in all treatments.

Conclusions

Straw and biochar amendments have different influences on anaerobic ammonia oxidation and denitrification within paddy soil. Our results suggested that the changes in denitrification and anammox rates in the biochar and straw treatments were mainly linked to functional gene abundance rather than microbial community structure and that denitrification played the more major role in N₂ production in paddy soil.

     

Effect of grazing intensity on protozoan community,microbial biomass,and enzyme activity in an alpine meadow on the Tibetan Plateau

Purpose

The alpine meadow has received mounting attention due to its degradation resulting from overgrazing on the Tibetan Plateau. However, belowground biotic characteristics under varied grazing stresses in this ecosystem are poorly understood.

Materials and methods

Here, the responses of soil protozoan abundance, community composition, microbial biomass, and enzyme activity to five grazing patterns including (1) artificial grassland without grazing (AG), (2) winter grazing (WG), (3) grazing for 7 months within a fence (GF), (4) continuous grazing for a whole year (CG), and (5) natural heavy grazing (HG) were investigated for two continuous years. Soil protozoan community composition was investigated using the most possible number (MPN) method, and soil microbial biomass and enzyme activity were analyzed using chloroform fumigation extraction and substrate utilization methods, respectively. Multivariate statistical analysis, the analysis of variance (ANOVA), multiple comparisons, and correlation analysis were together performed.

Results and discussion

The WG treatment had the highest abundance of total protozoa (2342–2524 cell g^?1). Compared with AG treatment, HG treatment significantly reduced the abundance of soil total, flagellate and ciliate protozoa, and protease activities in 2012 and 2013. Significantly, lower soil microbial biomass nitrogen (MBN) was also observed in the HG (6.60 and 14.6 mg N kg^?1) than those in other four treatments (22.3–82.9 mg N kg^?1) both in 2012 and 2013, whereas significantly higher microbial biomass carbon (MBC) was observed in HG than that in AG treatment in 2012. Moreover, significantly positive correlations were detected between the abundance of soil protozoa and soil moisture, pH, organic C, total N, and MBN. Our results indicated that soil protozoa showed a negative response to increasing grazing intensities and therefore, suggesting that aboveground grazing practices also exerted strong impact on belowground protozoa, not only on soil microbial characteristics.

Conclusions

Soil protozoan community composition was apparently different between the HG treatment and other four grazing patterns and was potentially impacted by altered soil properties and MBC and/or MBN. Our results suggested that moderate grazing may sustain better belowground biotic diversity and ecosystem functioning in this alpine meadow on the Tibetan Plateau.

     

Biochar for crop production: potential benefits and risks

Purpose

Biochar, the by-product of thermal decomposition of organic materials in an oxygen-limited environment, is increasingly being investigated due to its potential benefits for soil health, crop yield, carbon (C) sequestration, and greenhouse gas (GHG) mitigation.

Materials and methods

In this review, we discuss the potential role of biochar for improving crop yields and decreasing the emission of greenhouse gases, along with the potential risks involved with biochar application and strategies to avoid these risks.

Results and discussion

Biochar soil amendment improves crop productivity mainly by increasing nutrient use efficiency and water holding capacity. However, improvements to crop production are often recorded in highly degraded and nutrient-poor soils, while its application to fertile and healthy soils does not always increase crop yield. Since biochars are produced from a variety of feedstocks, certain contaminants can be present. Heavy metals in biochar may affect plant growth as well as rhizosphere microbial and faunal communities and functions. Biochar manufacturers should get certification that their products meet International Biochar Initiative (IBI) quality standards (basic utility properties, toxicant assessment, advanced analysis, and soil enhancement properties).

Conclusions

The long-term effects of biochar on soil functions and its fate in different soil types require immediate attention. Biochar may change the soil biological community composition and abundance and retain the pesticides applied. As a consequence, weed control in biochar-amended soils may be difficult as preemergence herbicides may become less effective.

     

Impacts of sea-level rise on sediment microbial community structure and function in two New England salt marshes,USA

Purpose

There is growing evidence for a tight linkage between the structure and function of microbial communities and for the importance of this relationship in ecosystem responses to disturbances such as sea-level rise (SLR). While the role of plants in determining the capacity of salt marshes to keep pace with SLR through sediment accretion has received considerable attention, the role of microbes in offsetting these gains via decomposition is less understood.

Materials and methods

We conducted a controlled experiment to determine the structural and functional responses of microbes to SLR, using soil from the low intertidal zone of two New England salt marshes in Massachusetts and New Hampshire, USA. We used terminal restriction fragment length polymorphisms (t-RFLPs) generated from microbial 16S rDNA to evaluate community composition and diversity and focused on changes in respiration with SLR, measured as total respired carbon normalized by percent organic matter, as a surrogate for decomposition rate.

Results and discussion

We observed a 24% reduction in microbial respiration with a simulated rise in sea level of 40 cm. This functional change was accompanied by a structural shift in microbial community composition among samples from New Hampshire but not Massachusetts, assessed via principal coordinate analysis of t-RFLP data. We also found greater microbial diversity within our New Hampshire samples, suggesting that low diversity may constrain community compositional shifts.

Conclusions

Our results suggest that decreased microbial respiration could alleviate the negative effects of SLR on salt marsh surface elevation, at least in the short term, and that the diversity of the soil microbial community may positively influence functional responses such as respiration.

     

The effect of landslide on soil organic carbon stock and biochemical properties of soil

Purpose

The aim of the study was to present variability of content and quality of soil organic matter on the landslide surface. Attempts were made to demonstrate the progress of the process of soil cover restoration 7 years after the landslides and biochemical activity of soil associated with the restoration of soil cover.

Materials and methods

The landslide area was located in southern Poland, in the Sucha Forest District. The soil properties were studied on a regular grid of points, which covered the entire area of the landslide. In soil samples, particle size, soil aggregates content, pH, total carbon and nitrogen content, microbial biomass carbon and nitrogen and the activity of dehydrogenases were determined. Additionally, the fractions of soil organic matter were used in the study as an indicator of soil quality due to the many important interactions of these components in the soil system.

Results and discussion

This study identified the landslide area as characterised by a stronger diversification of physical, chemical, and biological properties. The upper part of the landslide (in the area referred to as the landslide niche) is strongly eroded and characterised by the least advanced soil cover recovery. Additionally, low soil organic matter content was observed in the upper part of the landslide, which restricted biological activity of the studied soils. Soil microbial biomass carbon increased with restoration of landslide soils.

Conclusions

The soil organic matter plays a key role for the initial stage of soil formation on a landslide. The amount of soil organic matter on the studied landslide had a positive effect on the microbial biomasses C and N, dehydrogenases activity. Estimating the soil organic matter fraction can be utilised as an indicator of changes in soil.

     

Patterns and drivers of fungal diversity along an altitudinal gradient on Mount Gongga,China

Purpose

Fungi are essential components of soil microbial communities and have a crucial role in biogeochemical processes. Alpine regions are sensitive to climate change, and the importance of changes in fungal community composition along altitudinal gradients in alpine regions is hotly debated.

Materials and methods

We used 454 pyrosequencing approaches to investigate the fungal communities at 1600, 2300, 2800, 3000, and 3900 m above sea level along an altitudinal gradient on Mount Gongga.

Results and discussion

The results showed that Agaricomycetes, Sordariomycetes, and Tremellomycetes are the dominant classes at all sampling sites. Operational taxonomic unit richness decreased with increasing altitude, and the fungal communities were clustered into three groups that corresponded to altitudes of, i.e., 1600, 2300, and above 2800 m. The evenness of fungi was not significantly correlated with altitude, whereas beta diversities were significantly correlated with altitude. The distance-based redundancy analysis and Mantel test indicated that the composition of fungal assemblages was mostly driven by altitude and temperature.

Conclusions

Our results indicated that ecological processes possibly related to altitude and temperature play an important role in structuring fungal biodiversity along the elevational gradient. Our results highlight that different microbes may respond differently to environmental gradients.

     

Effects of vermicompost amendment as a basal fertilizer on soil properties and cucumber yield and quality under continuous cropping conditions in a greenhouse

Purpose

We examined the effects of vermicompost application as a basal fertilizer on the properties of a sandy loam soil used for growing cucumbers under continuous cropping conditions when compared to inorganic or organic fertilizers.

Materials and methods

A commercial cucumber (Cucumis sativus L.) variety was grown on sandy loam soil under four soil amendment conditions: inorganic compound fertilizer (750 kg/ha,), replacement of 150 kg/ha of inorganic compound fertilizer with 3000 kg/ha of organic fertilizer or vermicompost, and untreated control. Experiments were conducted in a greenhouse for 4 years, and continuous planting resulted in seven cucumber crops. The yield and quality of cucumber fruits, basic physical and chemical properties of soil, soil nutrient characteristics, and the soil fungal community structure were measured and evaluated.

Results and discussion

Continuous cucumber cropping decreased soil pH and increased electrical conductivity. However, application of vermicompost significantly improved several soil characteristics and induced a significant change in the rhizosphere soil fungal community compared to the other treatments. Notably, the vermicompost amendments resulted in an increase in the relative abundance of Ascomycota, Chytridiomycota, Sordariomycetes, Eurotiomycetes, and Saccharomycetes, and a decrease in Glomeromycota, Zygomycota, Dothideomycetes, Agaricomycetes, and Incertae sedis. Compared to the organic fertilizer treatment, vermicompost amendment increased the relative abundance of beneficial fungi and decreased those of pathogenic fungi. Cucumber fruit yield decreased yearly under continuous cropping conditions, but both inorganic and organic fertilizer amendments increased yields. Vermicompost amendment maintained higher fruit yield and quality under continuous cropping conditions.

Conclusions

Continuous cropping decreased cucumber yield in a greenhouse, but basic fertilizer amendment reduced this decline. Moreover, basal fertilizer amendment decreased beneficial and pathogenic fungi, and the use of vermicompost amendment in the basic fertilizer had a positive effect on the health of the soil fungal community.

     

Dissolved organic matter,nutrients, and bacteria in Antarctic soil core from Schirmacher Oasis

Purpose

This study focuses on the application of HPLC in dissolved organic matter (DOM) research in Antarctic environment together with nutrients and heterotrophic bacteria (HB) analyses. The specific aims were to investigate changes in DOM components characteristics and in nutrients in soil core from ground active layer and upper permafrost, to relate obtained data to active heterotrophic bacteria records after applying statistical data treatment methods, and to explore the potential impact of environment.

Materials and methods

A single Antarctic 1.9-m deep soil core drilled at a site without human impact from Schirmacher Oasis, located 70° 46′ 02″ S and 11° 45′ 11″ E, was explored. The chromophoric DOM (CDOM) was characterized by soil water analysis using multi-wavelength HPLC. Total organic carbon and total nitrogen were determined by elemental analysis, the total phosphorus by inductively coupled plasma spectrometry. The vertical changes in those nutrients and their ratios were investigated. The microbiological analysis was accomplished through the determination of psychrotrophic and psychrophilic aerobic HB numbers by colony-forming units counting method, and by epifluorescence microscopy examination. Cluster analysis using the Ward method and principal component analysis was performed on the chromatographic and microbiology data to reveal similar layers in studied soil core.

Results and discussion

In active soil layer, the CDOM was missing thus indicating rather active decomposition of organic material or organic debris by the local microbial community. In deep permafrost layers, the quantity of CDOM preserved in soil water increased. The content of total organic carbon in soil was low, between 0.05 and 0.2%, and decreased down the core. The vertical changes in nutrients (total N and P), the ratios C/N and C/P, followed total organic carbon profile suggesting similar sources. Microbiological analyses showed decreasing vertical concentrations of active HB. Statistical data treatment methods enabled clustering of soil core into three zones according to depth.

Conclusions

The obtained results contribute to better understanding of organic carbon-related processes in an almost un-polluted Antarctic environment. The CDOM, macronutrients, C/N, C/P, and HB profile characteristics of the Antarctic soil core clearly demonstrate the effect of environment (active or permafrost soil layers). The study demonstrated that combining HPLC with multi-wavelength detection and microbial analyses with statistical data treatment is potentially a promising tool of investigating changes in Antarctic soil DOM and in soil waters generally.

     

Stability of soil organic carbon and potential carbon sequestration at eroding and deposition sites

Purpose

This study aims to explore the dynamics of the factors influencing soil organic carbon (SOC) sequestration and stability at erosion and deposition sites.

Materials and methods

Thermal properties and dissolved aromatic carbon concentration along with Al, Fe concentration and soil specific surface area (SSA) were studied to 1 meter depth at two contrasting sites.

Results and discussion

Fe, Al concentrations and SSA size increased with depth and were negatively correlated with SOC concentration at the erosion site (P?<?0.05), while at the deposition site, these values decreased with increasing depth and were positively correlated with SOC concentration (P?<?0.05). TG mass loss showed that SOC components in the two contrasting sites were similar, but the soils in deposition site contained a larger proportion of labile organic carbon and smaller quantities of stable organic carbon compared to the erosion site. SOC stability increased with soil depth at the erosion site. However, it was slightly variable in the depositional zone. Changes in SUVA₂₅₄ spectroscopy values indicated that aromatic moieties of DOC at the erosion site were more concentrated in the superficial soil layer (0–20 cm), but at the deposition site they changed little with depth and the SUVA₂₅₄ values less than those at the erosion site.

Conclusions

Though large amounts of SOC accumulated in the deposition site, SOC may be vulnerable to severe losses if environmental conditions become more favorable for mineralization in the future due to accretion of more labile carbon. Deep soil layers at the erosion site (>30 cm deep) had a large carbon sink potential.

     

Influence of organic and inorganic passivators on Cd and Pb stabilization and microbial biomass in a contaminated paddy soil

Purpose

Soil contamination with heavy metals, such as Cd and Pb, has caused severe health and environmental risks all over the world. Possible eco-friendly solutions for Cd and Pb immobilization were required to reduce its mobility through various cost-effective amendments.

Materials and methods

A laboratory incubation study was conducted to assess the efficiency of biochar (BC), zeolite (ZE), and rock phosphate (RP) as passivators for the stabilization of Cd and Pb in paddy soil as well as soil microbial biomass. Various extraction techniques were carried out: a sequential extraction procedure, the European Community Bureau of Reference (BCR), toxicity characteristic leaching procedure (TCLP) test, and single extraction with CaCl₂. The impact of passivators on soil pH, dissolved organic carbon (DOC), and microbial biomass (carbon, nitrogen, and phosphorus) was examined in the metal contaminated soil.

Results and discussion

The results showed that the exchangeable portion of Cd in soil was significantly reduced by 34.8, 21.6, and 18.8% with ZE, RP, and BC at a 3% application rate, respectively. A similar tendency of reduction in Pb soluble portion was observed by ZE (9.6%), RP (20%), and BC (21.4%) at a 3% application rate. Moreover, the TCLP leachate of Cd and Pb was apparently reduced by 17 and 30.3% with BC at a 3% application dose, respectively, when compared to the control. Soil pH, nutrients, and microbial biomass C, N, and P were significantly increased with the addition of BC, RP, and ZE passivators.

Conclusions

The results showed that the incorporation of BC, ZE, and RP significantly reduced the Cd and Pb mobility in paddy soil as well as enhanced soil nutrients and microbial biomass. Overall, among all the amendments, rice straw derived-BC performed better for Cd and Pb immobilization in paddy soil.

     

Verrucomicrobial elevational distribution was strongly influenced by soil pH and carbon/nitrogen ratio

Purpose

The bacterial phylum Verrucomicrobia plays important roles in biogeochemical cycling processes, while the ecology of this phylum is still unclear. Previous elevational studies mainly focused on whole bacterial communities, while no study exclusively picked out Verrucomicrobia. Our objectives were to investigate the abundance, diversity and community composition of soil Verrucomicrobia across an elevation gradient on Changbai Mountain.

Materials and methods

In total, 24 soil samples representing six elevation gradients were collected. Primer set 515F/806R was used for PCR amplifications and sequencing was conducted on an Illumina HiSeq2000 platform. Data sets comprising of Verrucomicrobial phylum were culled from all quality sequences for the further analyses of Verrucomicrobial diversity and community composition.

Results and discussion

The relative abundance of Verrucomicrobia accounted for ~20% of the total bacterial communities, and Spartobacteria and DA101 were the most dominant class and genus, respectively. Verrucomicrobia community composition differed significantly among elevations, while the Verrucomicrobia diversity showed no apparent trend along elevation although the richness of some classes or genera significantly changed with elevation. The Verrucomicrobial community composition, diversity, and relative abundance of specific classes or genera were significantly correlated with soil pH and carbon/nitrogen ratio (C:N ratio).

Conclusions

These results indicated that Verrucomicrobia were abundant in Changbai Mountain soils, and Verrucomicrobial elevational distribution was strongly influenced by soil pH and C:N ratio. Our results also provide potential evidence that the dominant genus DA101 occupies different ecological niches and performs oligotrophic life history strategy in soil environment.

     

Soil nitrogen availability alters rhizodeposition carbon flux into the soil microbial community

Purpose

Soil microorganisms are important in the cycling of plant nutrients. Soil microbial biomass, community structure, and activity are mainly affected by carbon substrate and nutrient availability. The objective was to test if both the overall soil microbial community structure and the community-utilizing plant-derived carbon entering the soil as rhizodeposition were affected by soil carbon (C) and nitrogen (N) availability.

Materials and methods

A ¹³C-CO₂ steady-state labeling experiment was conducted in a ryegrass system. Four soil treatments were established: control, amendment with carboxymethyl cellulose (CMC), amendment with ammonium nitrate (NF), combined CMC and NF. Soil phospholipid fatty acid (PLFA) and ¹³C labeling PLFA were extracted and detected by isotope ratio mass spectrometer.

Results and discussion

The combined CMC and NF treatment with appropriate C/N ratio (20) significantly enhanced soil microbial biomass C and N, but resulted in lower soil inorganic N concentrations. There was no significant difference in soil PLFA profile pattern between different treatments. In contrast, most of the ¹³C was distributed into PLFAs 18:2ω6,9c, 18:1ω7c, and 18:1ω9c, indicative of fungi and gram-negative bacteria. The inorganic-only treatment was distinct in ¹³C PLFA pattern from the other treatments in the first period of labeling. Factor loadings of individual PLFAs confirmed that gram-positive bacteria had relatively greater plant-derived C contents in the inorganic-only treatment, but fungi were more enriched in the other treatments.

Conclusions

Amendments with CMC can improve N transformation processes, and the ryegrass rhizodeposition carbon flux into the soil microbial community is strongly modified by soil N availability.

     

Assessing soil microbial respiration capacity using rDNA- or rRNA-based indices: a review

Purpose

Understanding soil heterotrophic respiration in relation to microbial properties is not only fundamental to soil respiration modelling, prediction, and regulation through management, but also essential to interpreting microbial community dynamics from an ecologically meaningful perspective. This paper reviewed the recent advances in knowledge and proposed future directions for exploring the respiration-microbe relationships by means of rDNA- or rRNA-based indices (i.e. rDNA copies, rRNA copies, and rDNA- or rRNA-based community structures).

Materials and methods

We first elucidated the theoretical basis for using rDNA- or rRNA-based indices to probe into soil microbial respiration. Then, the published studies that simultaneously measured soil microbial respiration and the rDNA- or rRNA-based indices were synthesized, extracted, and analysed to further explore the respiration-microbe relationships. At last, the uncertainties and perspectives for establishing the respiration-microbe links were proposed and discussed.

Results and discussion

The rDNA- or rRNA-based indices are theoretically promising for pinpointing the relationships between soil heterotrophic respiration and microbial properties. Our systematic review suggested that the correlations between bacterial rDNA copies and microbial respiration are inconsistent across studies, while the fungal and archaeal rDNA (or ITS) copies showed moderately positive and negative correlations with soil microbial respiration, respectively. Bacterial 16S rDNA-based community structures were significantly correlated with soil microbial respiration in some studies, but not in some short-term situations. Although rRNA copies are widely used as the proxies of microbial activity, no significant correlations between rRNA copies and soil microbial respiration have been found in previous studies. Bacterial 16S rRNA-based community structures were correlated well with the short-term responses of soil microbial respiration to rewetting or labile carbon amendments and clearly outperformed other rDNA- or rRNA-based indices. As respiration-microbe relationships can be affected by many factors, such as soil physicochemical properties and even the analysis methods of microbial indices, the 69 previous studies included in this review actually provided limited information on them, and the aforementioned results still need to be further confirmed in future studies.

Conclusions and perspectives

Overall, the relationships between soil microbial respiration and rDNA- or rRNA-based indices are still far from being well established. Future research should be directed to systematically understanding the respiration-microbe links, with more attention to the fungus-, archaea- and RNA-related molecular indices. The relationships between microbial specific lineages and total respiration rates should be explored in future studies, and the effects of edaphic properties on the respiration-microbe relationships should also be evaluated.

     

Phosphine-induced phosphorus mobilization in the rhizosphere of rice seedlings

Purpose

The aim of this study was to evaluate the role of phosphine in the mobilization of phosphorus in the rhizosphere soil of rice seedlings and to determine the relative efficiency of phosphine in plant P acquisition.

Materials and methods

An indoor simulation experiment was conducted and the matrix-bound phosphine (MBP), phosphorus fractions, and phosphatase activity in the rhizosphere soil samples from rice cultivation, biomass, the plant P, and the root system activity were measured under different phosphine concentrations (0, 1.4, 4.2, and 7.0 mg m^?3) for a period of 30 days.

Results and discussion

The results indicated that phosphine treatments enhanced MBP, inorganic P (resin–P_i, NaHCO₃–P_i, and NaOH–P_i), and phosphatase activity, as well as the root system activity, and the content of P in the rice seedlings was stimulated with increasing phosphine concentrations. However, organic P (NaHCO₃–P_o and NaOH–P_o) accumulation occurred in the rhizosphere of the rice seedlings. In addition, the content of organic P in the soil samples decreased with increased phosphine concentration.

Conclusions

Therefore, relatively high concentrations of phosphine in paddy field could have a positive impact on the effectiveness of phosphorus in rice plants via influencing the rhizosphere properties.

     

Effect of nanoparticles on crops and soil microbial communities

Purpose

Nanoparticles (NPs) have received increased attention in recent past due to their unique distinct properties. Metal-based NPs are widely used in chemical and allied sector. Most of the research is directed to study the efficiency of NPs in medicine and agriculture. The aim of this review is to explore the possible threats posed by toxicity of various NPs on plants and microbial diversity.

Materials and methods

First, major sources of NPs to the environment were analyzed. The effects of metal-based NPs on the microbiota and plants are presented in this review. The results obtained by the authors during last 12 years of research are used.

Results and discussion

The exposure of soil to nanoparticles causes a decrease in soil microbial biomass and enzymatic activity, which impacts microbial community composition including yeasts, bacteria, fungi, and biological diversity. The effects of NPs on plants result in various types of abnormalities. Nanoparticles can also pose risks to human health.

Conclusions

Increased applications of NPs pose a threat to beneficial microbial communities as well as crops and soils. Thus, it is important to explore whether NPs could compromise crop yield, soil properties, soil organisms, and functional activities of soil.