Bioorganic fertilizer maintains a more stable soil microbiome than chemical fertilizer for monocropping

Understanding the responses of soil microbiome composition to various farming practices is important for selecting suitable managements to maintain soil functions. In this study, the influences of heavy chemical fertilizer application (CF) and reduced chemical fertilizer supplemented with organic (OF) or bioorganic fertilizer (BF, BF = OF + Trichoderma) on composition of soil microbiome were investigated for monocropping cucumber systems using a five-season continuous pot experiment. The MiSeq sequencing data indicated that the CF treatment resulted in the lowest fungal diversity and the BF treatment resulted in a relatively higher one close to the initial soil (CK). The BF and OF treatments had similar impacts on the composition of bacterial community, and the CF treatment significantly reduced bacterial diversity. Although both OF and BF treatments had better plant growth responses, they had less disturbance on the composition of fungal community relative to the CF treatment. The BF treatment is more predictable than the other treatments for postponing fungal diversity as the inoculated fungal species significantly (p < 0.05) affected the fungal community. In conclusion, the combination of bioorganic fertilizers with reduced chemical fertilizer application can maintain a diverse soil microbiome in cucumber monocropping.     

Long-term alternative dairy manure management approaches enhance microbial biomass and activity in perennial forage grass

Removing solids from liquid dairy manure slurry reduces manure phosphorus (P) and increases the available (mineral) fraction of nitrogen (N) but also decreases the organic matter content of the manure. While this novel treatment reduces environmental concerns associated with excess N and P application to soils, it may also reduce microbial biomass and activity in soil. This study evaluated the long-term effects of this alternative manure treatment compared to more typical nutrient applications in a perennial grass sward (tall fescue, Festuca arundinacea Schreb.) on soil microbial biomass, community composition, hydrolytic enzyme activity, and forage yield. Nutrient treatments for this long-term field experiment in Agassiz, British Columbia, Canada were started in 2003. The treatments included liquid dairy manure slurry, liquid dairy manure with solids removed, commercial fertilizer, a combination of fertilizer and dairy manure, and a control. All treatments were applied at 400–600 kg total N ha^?1 year^?1 in four equal doses. Soil microbial community composition (phospholipid fatty acid analysis) and activity (hydrolytic enzyme activity) were determined several times during the 2013 and 2014 growing seasons to a depth of 15 cm. Time of sampling (date) had a strong influence on microbial biomass, community composition, and activity, while the response to soil properties and yield was more varied. All manure treatments (dairy manure slurry, liquid fraction, and the combination) increased microbial biomass (by 19–32%) and the potential activity of cellulose-degrading enzymes (by 31–47%) compared to commercial fertilizer and unamended plots. The commercial fertilizer and liquid fraction lowered fungal/bacterial ratios compared with both whole manure and unamended plots. Our results indicate that separating the solid from the liquid fraction of manure, to improve crop yield and reduce P loading, did not reduce microbial community size and activity and that all manure treatments increased microbial biomass and activity compared to mineral fertilizer application.     

<Emphasis Type="Italic">Trichoderma</Emphasis> improves the growth of <Emphasis Type="Italic">Leymus chinensis</Emphasis>

Bio-fertilizer application has been proposed as a strategy for enhancing soil fertility, regulating soil microflora composition, and improving crop yields, and it has been widely applied in the agricultural yields. However, the application of bio-fertilizer in grassland has been poorly studied. We conducted in situ and pot experiments to investigate the practical effects of different fertilization regimes on Leymus chinensis growth, with a focus on the potential microecological mechanisms underlying the responses of soil microbial composition. L. chinensis biomass was significantly (P?<?0.05) increased by treatment with 6000 kg ha^?1 of Trichoderma bio-fertilizer compared with other treatments. We found a positive (R² =?0.6274, P <?0.001) correlation between bacterial alpha diversity and L. chinensis biomass. Hierarchical cluster analysis and nonmetric multidimensional scaling (NMDS) revealed that soil bacterial and fungal community compositions were all separated according to the fertilization regime used. The relative abundance of the most beneficial genera in bio-fertilizer (BOF) (6000 kg ha^?1Trichoderma bio-fertilizer) was significantly higher than in organic fertilizer (OF) (6000 kg ha^?1 organic fertilizer) or in CK (non-amend fertilizer), there the potential pathogenic genera were reduced. There were significant negative (P?<?0.05) correlations between L. chinensis biomass and the relative abundance of several potential pathogenic genera. However, the relative abundance of most beneficial genera were significantly (P?<?0.05) positively correlated with L. chinensis biomass. Soil properties had different effects on these beneficial and on these pathogenic genera, further influencing L. chinensis biomass.     

Effects of cover crop in an apple orchard on microbial community composition,networks, and potential genes involved with degradation of crop residues in soil

Changes in the soil microbial communities and networks were monitored after planting the cover crop for 9 years. The field experiment included plots with a cover crop and without a cover crop but with weed control, and two subplots with or without chemical fertilizer (192 kg N ha^?1, 108 kg P₂O₅ ha^?1, and 168 kg K₂O ha^?1 each year). After applying the cover crop and chemical fertilizer for 9 years, the composition and activity of bacterial and fungal communities changed significantly (p?<?0.05), with the cover crop had greater effects than the chemical fertilizer on the composition of the soil microbial community. The relative abundances of 22 selected genera (in Firmicutes and Bacteroidetes) and two selected classes (Ascomycota) related to cover crop residue degradation increased significantly in the presence of the cover crop (p?<?0.05). Network analysis showed that the cover crop decreased the number of positive links between bacterial and fungal taxa by 25.33%, and increased the negative links by 22.89%. The positive links among bacterial taxa increased by 16.63% with the cover crop, mainly among Proteobacteria (increase of 39), Firmicutes (16), Actinobacteria (five), and Bacteroidetes (10). The links among fungal taxa were less than among bacterial taxa and were not significantly affected by cover crop. Taxa such as Thaumarchaeota, unidentified_Nitrospiraceae, unidentified_Nitrosomonadaceae, Faecalibacterium, Coprococcus_3, and Ruminococcaceae_NK4A214_group dominated the network without the cover crop but they were not dominant with the cover crop. The relative abundances of potential genes involved with the degradation of cellulose, hemicellulose, and cello-oligosaccharides increased significantly with the cover crop. Therefore, the SOC and TN contents were enhanced by the cover crop with the increase of the soil enzyme activities. Thus, the apple yield was improved by the cover crop.     

Altered precipitation seasonality impacts the dominant fungal but rare bacterial taxa in subtropical forest soils

How soil microbial communities respond to precipitation seasonality change remains poorly understood, particularly for warm-humid forest ecosystems experiencing clear dry-wet cycles. We conducted a field precipitation manipulation experiment in a subtropical forest to explore the impacts of reducing dry-season rainfall but increasing wet-season rainfall on soil microbial community composition and enzyme activities. A 67% reduction of throughfall during the dry season decreased soil water content (SWC) by 17–24% (P < 0.05), while the addition of water during the wet season had limited impacts on SWC. The seasonal precipitation redistribution had no significant effect on the microbial biomass and enzyme activities, as well as on the community composition measured with phospholipid fatty acids (PLFAs). However, the amplicon sequencing revealed differentiated impacts on bacterial and fungal communities. The dry-season throughfall reduction increased the relative abundance of rare bacterial phyla (Gemmatimonadetes, Armatimonadetes, and Baoacteriodetes) that together accounted for only 1.5% of the total bacterial abundance by 15.8, 40, and 24% (P < 0.05), respectively. This treatment also altered the relative abundance of the two dominant fungal phyla (Basidiomycota and Ascomycota) that together accounted for 72.4% of the total fungal abundance. It increased the relative abundance of Basidiomycota by 27.4% while reduced that of Ascomycota by 32.6% (P < 0.05). Our results indicate that changes in precipitation seasonality can affect soil microbial community composition at lower taxon levels. The lack of community-level responses may be ascribed to the compositional adjustment among taxonomic groups and the confounding effects of other soil physicochemical variables such as temperature and substrate availability.     

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.

     

Responses of soil microbial community to nitrogen fertilizer and precipitation regimes in a semi-arid steppe

Purpose

Changes of nitrogen (N) cycle caused by N fertilization and precipitation regimes have affected the key ecosystem structure and functions in temperate steppe, which may modify the structure of soil microbial communities involved in N transformation. This paper was designated to examine the response of soil ammonia oxidizers and denitrifiers to the N fertilization and precipitation regimes in a semi-arid steppe where N and water contents are major limiting factors of the grassland productivity.

Materials and methods

This study was based on a long-term N fertilization and precipitation regimes experiment in Inner Mongolia (116° 17′ 20″ E, 42° 2′ 29″ N). The treatments including CK (control), R (reduced precipitation), W (30% increase in precipitation), N (10 g N m^?2 y^?1), RN (reduced precipitation and 10 g N m^?2 y^?1), and WN (30% increase in precipitation and 10 g N m^?2 y^?1). Soil basic chemical properties and microbial activities were analyzed. Molecular methods were applied to determine the abundance, structure and diversity of ammonia oxidizers and denitrifiers. Statistical analysis detected the main and interactive effect of treatments on soil microbial communities and revealed the relationship between soil microbial community structures and environmental factors.

Results and discussion

N fertilization significantly increased ammonia-oxidizing bacteria (AOB) abundance. Ammonia-oxidizing archaea (AOA) community structure was markedly changed in N fertilizer treatment and strongly affected by soil pH, while soil nitrate and water content correlated with AOB community structure. Soil nitrate was the key factor influencing nirK gene community structure, while soil pH and water content explained much of the variations of nosZ gene community. AOB-amoA and nosZ gene community diversities were influenced by precipitation regimes and interaction of N fertilization and precipitation regimes, respectively.

Conclusions

N fertilization and precipitation regimes had significant influences on the changes of soil properties and microbial functional communities. Soil nitrification was mainly driven by AOB in the semi-arid grassland. Changes of substrate content and soil pH were the key factors in shifting functional microbial communities. The non-synergistic effects of N fertilization and precipitation regimes on the microbial functional groups indicated that the negative effect of lower pH induced by N fertilization would be alleviated by precipitation regimes, which should be well considered in grassland restoration.

     

Effects of nitrification inhibitor 3,4-dimethylpyrazole phosphate and fungicide iprodione on soil fungal biomass and community: based on internal transcribed spacer region

Purpose

Nitrification inhibitors that impact soil nitrifying microorganisms have been widely applied in agricultural soils to enhance the efficiency of nitrogen fertilizers. However, little is known about their combined impact with other chemical applications, such as fungicides, on soil fungi. This study specifically examined the effects of the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP), alone or together with the fungicide iprodione, on fungi biomass and community in a typical farmland soil.

Materials and methods

Four treatments were set: (1) control of zero agrochemical applications (CK), (2) a single DMPP application (DAA), (3) repeated iprodione applications (4×IPR), and (4) combined applications of DMPP and iprodione (DAA+4×IPR). The agrochemicals were applied at the recommended intervals, and the soil samples were incubated in the dark for 28 days. During the incubation, soil sample DNA was extracted, and the effects of DMPP and iprodione applications on soil fungal internal transcribed spacer (ITS) abundances were determined with quantitative PCR (qPCR). At the end of the incubation, Illumina MiSeq method was employed to assess soil fungal community diversity and structure.

Results and discussion

DMPP application had a negligible effect on fungal ITS abundance. However, repeated iprodione applications significantly decreased fungal ITS abundances. After 28 days of incubation, the fungal ITS abundances in the 4×IPR and DAA+4×IPR treatments were 43.6 and 56.2% of that measured from the CK treatment, respectively. Shannon indices of fungal communities demonstrated the treatment-induced gradients, with the DAA+4×IPR treatment harboring the highest Shannon index. Fungal community structures following the DAA and 4×IPR treatments remained overlapping with that in the CK treatment, but repeated iprodione applications markedly enriched the family Teratosphaeriaceae. Relative to the CK treatment, fungal community structure in the DAA+4×IPR treatment was significantly changed, with the families Cephalothecaceae, Hypocreaceae, and Cordycipitaceae harboring a linear discriminant analysis value >3.

Conclusions

DMPP application had negligible effects on soil fungal biomass, community diversity, and structure, potentially indicating that the DMPP is “bio-safe.” Conversely, repeated iprodione applications significantly decreased fungal ITS abundances. Moreover, the family Teratosphaeriaceae could be further investigated as a potential biomarker of the impacts of iprodione on soil fungi. The combined applications of DMPP and iprodione stimulated the Shannon diversity index and markedly changed soil fungal community structure.

     

Long-term P fertilisation of pasture soil did not increase soil organic matter stocks but increased microbial biomass and activity

The soil organic matter (OM) content of soils in a long-term fertiliser field trial (Winchmore, New Zealand) are similar (P > 0.05) despite >60 years application of different phosphorus (P) rates. As the net primary productivity increased with P addition, greater losses of carbon (C) occur concomitantly with increased P fertility. Several hypotheses have been proposed to explain the mechanisms, including C leaching, increased earthworm activity or elevated rates of microbial activity. In this study, we found support for both direct and secondary effects of soil P on soil C through impacts on the soil microbial community. Microbial biomass, inferred through quantification of hot water extractable C, increased with soil P status and decreased with C/P ratio (P < 0.001). However, the microbial biomass had no relationship with soil organic C content (P = 0.485). Mineralisation of C substrates added to soil also increased with soil P status (total P, R ² = 0.84; P < 0.001). These results indicated potential conditioning of the microbial community for rapid C cycling. Utilisation of different C compounds was clustered by cophenetic similarity; a distinct group of ten carbon compounds was identified for which rates of mineralisation were strongly associated with soil P status and microbial biomass. However, this alteration of microbial community size and activity was not reflected in abundances of selected oligotrophic and copiotrophic taxa. As such, the alteration may be due to changes in the abundances of all taxa, i.e. a general community response.     

Recovery of Amoebae Community in the Root Soil of <Emphasis Type="Italic">M. sativa</Emphasis> after a Strong Contamination Pulse with n-Hexane

Microbial food webs tolerate toxic compounds depending on individualistic species resistance and their ability of using alternate food sources. Soil polluted with low-molecular weight volatile organics, such as hexane, diminishes bacterial and fungal communities despite its short residence time. Survival of microbial species depends on perturbation intensity, which in turn restricts resources for amoebae survival in polluted soil. Soil functional recovery from anthropogenic perturbations depends on microbial organic matter (OM) metabolization of pollutants. However, reconfiguration of amoebae community after soil exposure remains largely unknown. A microcosms study was carried out to determine the effects of hexane on the community structure of soil amoebae as well as the importance of Medicago sativa on amoebae community recovering. Hexane had a negative impact on species richness and structure of the amoebae community 24 h after pollution. There was a significant increase in species richness and number of amoebae 30 days after contamination. These two parameters further increased after 60 days from contamination. After 30 days of the initial trophozoites extinction caused by Hexane, M. sativa’s. Root zone showed a significant increase of both species richness and number of individuals. This recovery trend was kept after 60 days when the highest values in species richness and abundance of individuals were shown in both polluted and non-polluted microcosms. In conclusion, M. sativa’s root zone speeds up recovery of the amoebae community structure after pollution exposure.     

Effects of saline water irrigation and fertilization regimes on soil microbial metabolic activity

Purpose

Irrigation and fertilization can change soil environment, which thereby influence soil microbial metabolic activity (MMA). How to alleviate the adverse effects by taking judicious saline water irrigation and fertilization regimes is mainly concerned in this research.

Materials and methods

Here, we conducted a field orthogonal designed test under different saline water irrigation amount, water salinity, and nitrogen fertilizer application. The metabolic profiles of soil microbial communities were analyzed by using the Biolog method.

Results and discussion

The results demonstrated that irrigation amount and fertilizer application could significantly change MMA while irrigation water salinity had no significant effect on it. Medium irrigation amount (30 mm), least (50 kg ha^?1) or medium (350 kg ha^?1) N fertilizer application, and whatever irrigation water salinity could obtain the optimal MMA. Different utilization rates of carbohydrates, amino acids, carboxylic acids, and polymers by soil microbial communities caused the differences of the effects, and D-galactonic acid γ-lactone, L-arginine, L-asparagine, D-glucosaminic acid, Tween 80, L-threonine, and D-galacturonic acid were the indicator for distinguishing the effects.

Conclusions

The results presented here demonstrated that by regulating irrigation water amount and fertilizer application, the effects of irrigation salinity on MMA could be alleviated, which offered an efficient approach for guiding saline water irrigation.

     

Effects of Endosulfan on the Populations of Cultivable Microorganisms and the Diversity of Bacterial Community Structure in Brunisolic Soil

Endosulfan, an organochlorine pesticide, has been applied ubiquitously worldwide. However, endosulfan has been identified as a type of persistent organic pollutants (POPs), and its ecotoxicity has drawn attentions from scientists. The present study was implemented to examine the effects of endosulfan on the diversity and structure of soil microorganism communities. A control treatment and three concentrations (0.1, 1.0, and 10.0 mg/kg) were set up in laboratory experiments and sampled on days 7, 14, 21, and 28. The results revealed that the populations of bacteria and actinomycetes decreased significantly after 1.0 and 10.0 mg/kg treatments and that the soil microbial biomass carbon (MBC) was increased by endosulfan compared with the control. Terminal restriction fragment length polymorphism (T-RFLP) results revealed that the soil bacterial diversity was decreased by endosulfan and that the soil microbial community structure became unstable after endosulfan application. Moreover, the results of a 16S rRNA clone library revealed that the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Spirochaetes, and Firmicutes showed an obvious advantage and closely relative. In conclusion, the results of the present study indicated that 0.1–10.0 mg/kg endosulfan showed obvious influences on the diversity and structure of the soil microbial community.     

Response of microbial diversity to C:N:P stoichiometry in fine root and microbial biomass following afforestation

Soil samples were collected in June and October from areas with three land-use types, i.e., Robinia pseudoacacia L. (RP), Caragana korshinskii Kom. (CK), and abandoned land (AL), of which the former two were afforested areas, whereas the latter was not. These areas were converted from similar farmlands 40 years prior. Illumina sequencing of 16S rRNA gene and fungal ITS gene was used to analyze soil bacterial and fungal diversity. Additionally, plant communities, soil properties, fine root biomass, and C, N, and P levels in fine root and microbial biomass were estimated. Compared to AL, the C:N:P stoichiometry in fine root and microbial biomass in the afforested lands was synchronously changed, especially the N:P ratio. Soil microbial diversities were affected by afforestation and were more related to N:P ratio than C:P and C:N ratios. Moreover, Alpha-proteobacteria, Gamma-proteobacteria, and Bacteroidetes were significantly more abundant in afforested soils than in the AL soil, and the abundances of Actinobacteria, Chloroflexi, Cyanobacteria, and Nitrospirae ranked as AL > RP or CK. For fungal taxa, Ascomycota abundance responded positively to afforestation, whereas Basidiomycota abundance responded negatively. Changes of soil microbial taxa were significantly correlated with the N:P ratio in fine root and microbial biomass, which explained 54.1 and 55% of the total variation in bacterial and fungal taxa, respectively. Thus, our results provide evidence that compositions of soil microbial communities are linked to the N:P ratio in the plant-soil system.     

Biochar amendment changes temperature sensitivity of soil respiration and composition of microbial communities 3 years after incorporation in an organic carbon-poor dry cropland soil

Topsoil samples were collected from plots in a dry cropland in the North China Plain 3 years after a single incorporation of biochar at 20 and 40 t ha^?1 and analyzed for abundances and composition of microbial community and for respiration under controlled laboratory conditions at 15, 20, and 25 °C. The addition of biochar generally reduced soil respirations at the three temperatures and the temperature sensitivity (Q₁₀) at 15–20 °C. Biochar amendment significantly increased bacterial 16S rRNA gene abundances and fungal ITS gene diversity and induced clear changes in their community compositions due to improvements in soil chemical properties such as soil organic C (SOC) and available N contents and pH. Illumina Miseq sequencing showed that the relative abundances of Actinobacteria, Gammaproteobacteria, Firmicutes, and Alternaria within Ascomycota, capable of decomposing SOC, were significantly decreased under biochar at 40 t ha^?1. The Q₁₀ values at 15–20 °C were significantly correlated with fungal diversity and dehydrogenase activity. Our results suggest that after 3 years a single biochar amendment could induce a shift in microbial community composition and functioning towards a slower organic C turnover and stability to warming, which may potentially reduce soil C loss in dryland under climate warming in the future.     

Changes in soil microbial substrate utilization in response to altered litter diversity and precipitation in a Mediterranean shrubland

This study aimed at quantifying the consequences of reduced precipitation and plant diversity on soil microbial community functioning in a Mediterranean shrubland of southern France. Across a natural gradient of shrub species diversity, we established a total of 92 plots (4 × 4 m) with and without a moderate rain exclusion treatment of about 12 % of total precipitation. Shrub diversity included all possible combinations of the four dominant species (Cistus albidus, Quercus coccifera, Rosmarinus officinalis, and Ulex parviflorus). Respective leaf litter mixtures of these species combinations were exposed in all plots over 2 years. We quantified how litter species richness and the reduction in precipitation affected the soil microbial substrate utilization (measured by CO₂ evolution using the MicroResp method) on soil samples collected underneath each individual litter mixture after 1 and 2 years of decomposition. Moderate precipitation reduction had a minor impact, but litter species richness and the dissimilarity in phenolic concentrations (estimated using Rao’s quadratic entropy) showed a positive effect on the diversity of substrates metabolized by the microbial communities. Moreover, litter species richness increased soil microbial activity by increasing the catabolic diversity of the soil microbial community. These effects were mostly driven by the presence of Quercus and Ulex leaf litter, which at the same time reduced microbial metabolic dominance, while the presence of Rosmarinus had opposite effects. Our data suggest that plant species loss can have stronger effects on the functioning of soil microbial communities than moderate drought, with potentially important feedbacks on biogeochemical cycling in Mediterranean shrubland ecosystems.     

Effects of long-term treatments of different organic fertilizers complemented with chemical N fertilizer on the chemical and biological properties of soils

Continuous cultivation has been known to decrease soil organic matter content. Application of organic matter to cultivated soil is an important practice from the point of view of maintaining an adequate amount of soil organic matter. Soil organic matter content significantly affects soil microbial activity, which is an important index of soil quality. In this study, a field experiment was conducted to examine the long-term effects of different kinds of organic matter in combination with inorganic nitrogen (N) fertilizer on chemical and biological properties of soils. There were seven treatments, namely (1) CK (without fertilization), (2) Chem-N (applying chemical N fertilizer only), (3) Comp (applying compost with the same rate of N as the Chem-N treatment), (4) Comp + l/3 N (applying compost complemented with 33% of the chemical N fertilizer of the Chem-N treatment), (5) Comp + 2/3 N (applying compost complemented with 66% of the chemical N fertilizer of the Chem-N treatment), (6) GM + 1/3 N (applying green manure complemented with 33% of the chemical N fertilizer of the Chem-N treatment) and (7) Peat + 1/3 N (applying peat complemented with 33% of the chemical N fertilizer of the Chem-N treatment). After continuous treatment for 12 years and with cultivation of 24 crops on the same area, soils were sampled for analyses of chemical and biological properties, enzymatic activities and phospholipid fatty acid (PLFA) profiles. The results showed that compared with CK and Chem-N treatments, applications of compost and peat increased soil organic carbon (SOC) content and altered microbial activities and microbial community structure. However, application of green manure for 12 years had no effect on SOC content. Both microbial activities and PLFA profiles were clearly dependent on the characteristics of the applied organic amendments. In summary, a peat application led to the highest increase in SOC content compared to compost and green manure; however, compost-treated soil had a higher microbial population and higher microbial and enzyme activities, while the effects of both green manure and chemical N fertilizer on soil properties were similar.     

Soil pre-fumigation could effectively improve the disease suppressiveness of biofertilizer to banana <Emphasis Type="Italic">Fusarium</Emphasis> wilt disease by reshaping the soil microbiome

Two seasonal pot experiments were conducted to investigate the effect of biofertilizer application after mixture of lime and ammonium bicarbonate (LA) fumigation, on banana Fusarium wilt disease suppression and soil microbial community composition. Biofertilizer application after LA fumigation decreased 80% of disease incidence compared to control of biofertilizer application to non-fumigated soil. Biofertilizer application after fumigation clearly manipulated soil microbial community composition as revealed by non-metric multidimensional scaling and Venn diagram. LA fumigation significantly reduced the abundance of F. oxysporum while biofertilizer application after fumigation could further decrease it. Furthermore, indigenous microbes, e.g., Bacillus, Pseudomonas, and Mortierella, were associated with disease suppression. Biofertilizer application after fumigation significantly (p?<?0.05) increased the soil pH and content of soil total C and available P and K, and this probably reshaped soil microbial community as revealed by redundancy analysis and variance partitioning analysis. The observed disease suppression due to biofertilizer application after soil fumigation can be attributed to the reduced abundance of F. oxysporum by general suppression resulting from manipulated soil properties and recovered soil microbiome.     

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.

     

Long-term impacts of manure, straw, and fertilizer on amino sugars in a silty clay loam soil under temperate conditions

There is increasing evidence that microorganisms participate in soil C sequestration and stabilization in the form of resistant microbial residues. The type of fertilizers influences microbial activity and community composition; however, little is known about its effect on the microbial residues and their relative contribution to soil C storage. The aim of this study was to investigate the long-term impact (21 years) of different fertilizer treatments (chemical fertilizer, crop straw, and organic manure) on microbial residues in a silty clay loam soil (Udolls, USDA Soil Taxonomy). Amino sugars were used to indicate the presence and origin of microbial residues. The five treatments were: CK, unfertilized control; NPK, chemical fertilizer NPK; NPKS₁, NPK plus crop straw; NPKS₂, NPK plus double amounts of straw; and NPKM, NPK plus pig manure. Long-term application of inorganic fertilizers and organic amendments increased the total amino sugar concentrations (4.4–8.4 %) as compared with the control; and this effect was more evident in the plots that continuously received pig manure (P?<?0.05). The increase in total amino sugar stock was less pronounced in the straw-treated plots than the NPKM. These results indicate that the accumulation of soil amino sugars is largely influenced by the type of organic fertilizers entering the soil. Individual amino sugar enrichment in soil organic carbon was differentially influenced by the various fertilizer treatments, with a preferential accumulation of bacterial-derived amino sugars compared with fungal-derived glucosamine in manured soil.     

Response of soil organic matter fractions and composition of microbial community to long-term organic and mineral fertilization

The effects of organic and mineral fertilization on four soil organic matter (SOM) fractions (non-protected, physically protected, chemically protected, and biochemically protected) and microbial community composition were investigated by sampling soil of a 35-year-long fertilization experiment. The SOM fractions were investigated by combined physical and chemical approaches, while microbial community composition was determined by phospholipid fatty acid analysis (PLFA). Organic C (SOC) was primarily distributed within the microaggregate-protected particulate organic matter (iPOM) and the hydrolysable and non-hydrolysable silt-sized (H-Silt, NH-Silt) fractions, which accounted for 11.6–16.9, 23.4–28.9, and 25.4–30.6% of the total SOC content, respectively. The contributions of these “slow” fractions (iPOM, H-Silt, NH-Silt) to the increased SOC were 178–293, 118–209, and 85–109% higher after long-term sole manure or manure in combination with inorganic N fertilization compared with unfertilized soil (control). The combination of manure and mineral fertilizers increased the coarse and fine non-protected C (cPOM and fPOM) contents much more (34.1–60.7%) than did manure alone. PLFAs, bacteria, G (+) bacteria, and actinomycete abundances were the highest in soil with manure, followed by soil treated with manure combined with mineral N. The addition of inorganic and organic fertilization both altered the microbial community composition compared with the control. All SOM fractions contributed to 81.1% of the variance of the PLFAs-related microbial community composition by direct and indirect effects. The change in coarse unprotected particulate organic matter (cPOM) was the major factor affecting soil microbial community composition (p < 0.001). Our study indicates that physical, chemical, and biochemical protection mechanisms are important in maintaining high SOC level after the addition of manure. A close linkage between soil microbial community composition and cPOM suggests that C availability is an important factor for influencing microbial composition after long-term inorganic and organic fertilization.