Elevated CO<Subscript>2</Subscript> alters the abundance but not the structure of diazotrophic community in the rhizosphere of soybean grown in a Mollisol

The effect of elevated CO₂ (eCO₂) on rhizospheric diazotrophic community in cropland has little been studied, although eCO₂ facilitates nodulation and N₂ fixation in legumes. In this study, four soybean cultivars (Xiaohuangjin, Suinong 8, Suinong 14, and Heinong 45) were grown in Mollisols for 65 days under ambient CO₂ (aCO₂) (390 ppm) or eCO₂ (550 ppm). Quantitative PCR and Illumina MiSeq sequencing targeting the nifH gene that reflects the composition of diazotrophic community were determined. Elevated CO₂ significantly increased the abundance of nifH gene copies in the rhizospheres of the Suinong 8 and Heinong 45 cultivars, but not in the Suinong 14 and Xiaohuangjin cultivars. The nifH abundance correlated negatively with nodule density (p?≤?0.01) but positively with nodule size (p?≤?0.01). Elevated CO₂ did not significantly alter the composition of diazotrophic community, nor shift dominant bacterial operational taxonomic units (OTUs). These results indicated that eCO₂ stimulated the growth but did not alter the community composition of diazotrophs in the rhizosphere of soybean, which depended on cultivar and might contribute to nodulation responses to eCO₂.     

Effects of biochar on Cd and Pb mobility and microbial community composition in a calcareous soil planted with tobacco

An experiment was conducted with tobacco (Nicotiana tabacum L.) grown in a Cd- and Pb-contaminated calcareous soil amended with 0.0, 1.0, 2.5, and 5.0% (w/w) tobacco stalk biochar (BC). The BC amendment significantly increased organic matter, total C, N, P, and K contents of soil, and the C/N ratio. Bioavailable metal concentrations (DTPA extraction) decreased by increasing BC application rate. The 5.0% BC amendment significantly decreased the DTPA-extractable Cd and Pb by 10.4 and 13.6%, respectively. Correspondingly, the bioaccumulation and translocation factors of Cd and Pb also decreased by increasing the BC addition rates and this indicated that BC inhibited the uptake and transfer of both Cd and Pb by tobacco plants. Moreover, high-throughput sequencing revealed that BC increased Chao1 richness, Shannon’s diversity and Simpson’s diversity of bacterial communities of soil. The relative abundance and genera composition of Adhaeribacter, Rhodoplanes, Pseudoxanthomonas, and Candidatus Xiphinematobacter increased under BC treatments, while those of Kaistobacter, Lacibacter, and Pirellula decreased. Overall, BC increased soil nutrients (C, N, P, and K contents), enhanced bacterial diversity indexes and richness, and changed the bacterial community composition, which may all have contributed to reduce the mobility and bioavailability of both Cd and Pb in a calcareous soil.     

Bacterial diversity in the rhizosphere of two phylogenetically closely related plant species across environmental gradients

Purpose

Rhizosphere soil bacterial communities are crucial to plant growth, health, and stress resistance. In order to detect how bacterial communities associated with the rhizosphere of phylogenetically related plant species vary in terms of composition, function, and diversity, we investigated the rhizosphere bacterial community structure of two perennial shrub species, Caragana jubata and Caragana roborovskyi, under natural field conditions in northwest China and analyzed the influence of soil properties and environmental factors.

Materials and methods

Eighteen root samples, eight for C. jubata, and ten for C. roborovskyi, along with any adherent soil particles, were collected from multiple sites in northwest China. The rhizosphere soil was washed from the roots, and bacterial communities were analyzed using Illumina MiSeq sequencing of 16S rRNA gene amplicons. Then, α-diversity and β-diversity were calculated using QIIME.

Results and discussion

Across species, Proteobacteria (29 %), Actinobacteria (15 %), Chloroflexi (10 %), Acidobacteria (10 %), Bacteroidetes (8 %), Firmicutes (8 %), Planctomycetes (7 %), Gemmatimonadetes (4 %), and Verrucomicrobia (3 %) were the most abundant phyla in the rhizosphere of C. jubata and C. roborovskyi. However, principal co-ordinates analysis indicated strong interspecific patterns of bacterial rhizosphere communities. Further, the richness of Proteobacteria, Acidobacteria, Bacteroidetes, Verrucomicrobia, Firmicutes, and Nitrospirae was significantly higher in the rhizosphere of C. jubata compared with C. roborovskyi, while the opposite was found for Actinobacteria and Cyanobacteria. However, the Shannon index showed no significant difference in α-diversity between C. jubata and C. roborovskyi. Distance-based redundancy analysis indicated that soil properties and environmental factors exerted strong influences on the structure of the rhizosphere bacterial community and explained 47 and 46 % of community variances between samples, respectively.

Conclusions

Our results showed strong interspecific clustering of the bacterial rhizosphere communities of C. roborovskyi and C. jubata. Altitude explained most of the variation in the composition of bacterial rhizosphere communities of C. roborovskyi and C. jubata, followed by soil pH, water content, organic matter content, total nitrogen content, and mean annual rainfall.

     

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.     

Bacterial community incorporating carbon derived from plant residue in an anoxic non-rhizosphere soil estimated by DNA-SIP analysis

Purpose

Plant residues are one of the main sources of soil organic matter in paddy fields, and elucidation of the bacterial communities decomposing plant residues was important to understand their function and roles, as the microbial decomposition of plant residues is linked to soil fertility. We conducted a DNA stable isotope probing (SIP) experiment to elucidate the bacterial community assimilating 13-carbon (¹³C) derived from plant residue under an anoxic soil condition. In addition, we compared the bacterial community with that under the oxic soil condition, which was elucidated in our previous study (Lee et al. in Soil Biol Biochem 43:814–822, 2011).

Materials and methods

We used the ¹³C-labeled dried rice callus cells as a model of rice plant residue. A paddy field soil was incubated with unlabeled and ¹³C-labeled callus cells. DNA extracted from the soils was subjected to buoyant density gradient centrifugation to fractionate ¹³C-enriched DNA. Then, polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) analysis of bacterial 16S rDNA band patterns and band sequencing method were used to evaluate bacterial community.

Results and discussion

DGGE analysis showed that the band patterns in the ¹³C-enriched fractions were distinctly changed over time, while the changes in the community structure before fractionation were minor. Sequencing of the ¹³C-labeled DGGE bands revealed that Clostridia were a major group in the bacterial communities incorporating the callus-derived carbon although Gram-negative bacteria, and Actinobacteria also participated in the carbon flow from the callus under the anoxic condition. The proportion of Gram-negative bacteria and Actinobacteria increased on 14 days after the onset of incubation, suggesting that the callus was decomposed by diverse bacterial members on this phase. When the bacterial groups incorporating the ¹³C were compared between under anoxic and oxic soil conditions, the composition was largely different under the two opposite conditions. However, some members of Gram-negative bacteria were commonly found under the anoxic and oxic soil conditions.

Conclusions

The majority of bacterial members assimilating the callus carbon was Clostridia in the soil under anoxic conditions. However, several Gram-negative bacterial members, such as Acidobacteria, Bacteroidetes, and Proteobacteria, also participated in the decomposition of callus under anoxic soil conditions. Our study showed that carbon flow into the diverse bacterial members during the callus decomposition and the distinctiveness of the bacterial communities was formed under the anoxic and oxic soil conditions.

     

Chemical nature of soil organic carbon under different long-term fertilization regimes is coupled with changes in the bacterial community composition in a Calcaric Fluvisol

Fertilization is an important factor influencing the chemical structure of soil organic carbon (SOC) and soil microbial communities; however, whether any connection exists between the two under different fertilization regimes remains unclear. Soils from a 27-year field experiment were used to explore potential associations between SOC functional groups and specific bacterial taxa, using quantitative multiple cross-polarization magic-angle spinning ¹³C nuclear magnetic resonance and 16S rRNA gene sequencing. Treatments included balanced fertilization with organic materials (OM) and with nitrogen (N), phosphorus (P), and potassium (K) mineral fertilizers (NPK); unbalanced fertilization without one of the major elements (NP, PK, or NK); and an unamended control. These treatments were divided into four distinct groups, namely OM, NPK, NP plus PK, and NK plus control, according to their bacterial community composition and SOC chemical structure. Soil total P, available P, and SOC contents were the major determinants of bacterial community composition after long-term fertilization. Compared to NPK, the OM treatment generated a higher aromatic C–O and OCH₃ and lower alkyl C and OCH abundance, which were associated with the enhanced abundance of members of the Acidobacteria subgroups 6 and 5, Cytophagaceae, Chitinophagaceae, and Bacillus sp.; NP plus PK treatments resulted in a higher OCH and lower aromatic C–C abundance, which showed a close association with the enrichment of unclassified Chloracidobacteria, Syntrophobacteraceae, and Anaerolineae and depletion of Bacillales; and NK plus control treatments resulted in a higher abundance of aromatic C–C, which was associated with the enhanced abundance of Bacillales. Our results indicate that different fertilization regimes changed the SOC chemical structure and bacterial community composition in different patterns. The results also suggest that fertilization-induced variations in SOC chemical structure were strongly associated with shifts in specific microbial taxa which, in turn, may be affected by changes in soil properties.     

Spatial patterns of microbial denitrification genes change in response to poultry litter placement and cover crop species in an agricultural soil

Subsurface-banding manure and winter cover cropping are farming techniques designed to reduce N loss. Little is known, however, about the effects of these management tools on denitrifying microbial communities and the greenhouse gases they produce. Abundances of bacterial (16S), fungal (ITS), and denitrification genes (nirK, nirS, nosZ-I, and nosZ-II) were measured in soil samples collected from a field experiment testing the combination of cereal rye and hairy vetch cover cropping with either surface-broadcasted or subsurface-banded poultry litter. The spatial distribution of genes was mapped to identify potential denitrifier hotspots. Spatial distribution maps showed increased 16S rRNA genes around the manure band, but no denitrifier hotspots. Soil depth and nitrate concentration were the strongest drivers of gene abundance, but bacterial gene abundance also differed by gene, soil characteristics, and management methods. Gene copy number of nirK was higher under cereal rye than hairy vetch and positively associated with soil moisture, while nirS gene copies did not differ between cover crop species. The nirS gene copies increased when manure was surface broadcasted compared to subsurface banded and was positively associated with pH. Soil moisture and pH were positively correlated to nosZ-II but not to nosZ-I gene copy numbers. We observed stronger correlations between nosZ-I and nirS, and nosZ-II and nirK gene copies compared to the reverse pairings. Agricultural management practices differentially affect spatial distributions of genes coding for denitrification enzymes, leading to changes in the composition of the denitrifying community.     

A hollow bacterial diversity pattern with elevation in Wolong Nature Reserve,Western Sichuan Plateau

Purpose

The pattern of eukaryotic macroorganisms varies with altitude is well-documented; by contrast, very little is known of how a bacterial pattern in soils varies with the elevation in a montane ecosystem. Mostly, previous studies on soil bacteria have either found a diversity decline, no trend, or a hump-back trend with increasing elevation. The aim of this study was to investigate the bacterial community composition and diversity patterns of Mount Nadu in Wolong Nature Reserve, Western Sichuan Plateau (3000–3945 masl).

Materials and methods

In total, 30 soil samples from the mountain at 10 sampling elevational zones (every 100 m from the baseband to the summit) were collected. High-throughput pyrosequencing approach was performed of soil bacterial 16S rRNA targeting V3?+?V4 region by MiSeq PE300 and taxonomically classified based on Silva database. Bacterial community composition and diversity patterns were detected, and bacterial data were correlated with environmental factors to determine which factors influenced bacterial community composition.

Results and discussion

We obtained an average of 30,172 sequences per soil and found that the relative abundance of Acidobacteria and Proteobacteria count more than 70 % of the whole bacteria. Cooperative network analysis also revealed that Acidobacteria and Proteobacteria were important hubs in the community. Bacterial diversity pattern was found to be a significant hollow trend along altitudinal gradients and diversity of the dominant phyla (e.g., Acidobacteria, Proteobacteria) followed the results of the whole bacterial diversity. Moreover, distance-based linear model identified that soil pH and TN significantly provided 7.40 and 6.01 % of the total variation.

Conclusions

The hollow trend of bacterial diversity has rarely been observed in nature. It indicated that no unifying bacterial diversity pattern can be expected along elevational gradients among the mountain system, and our result suggested the importance of environmental factors in structuring bacterial communities in this montane ecosystem.

     

Abundance and diversity of sulphur-oxidising bacteria and their role in oxidising elemental sulphur in cropping soils

There is an increasing interest in elemental S as a S fertiliser source, but to be available to plants, elemental S has to be oxidised to sulphate. Elemental S oxidation is known to be affected by soil properties and environmental conditions, but it is still unclear if elemental S oxidation is related to the abundance and diversity of S-oxidising bacteria in cropping soils. In this study, we investigated the abundance and diversity of S-oxidising bacteria by targeting a functional gene (soxB) and assessed their relationship with elemental S oxidation in ten cropping soils. Positive correlations between soil C, N and S contents on the one hand and the abundances of soxB and 16S ribosomal deoxyribonucleic acid (rRNA) genes on the other suggested that the abundances of S oxidising bacteria in particular and of bacteria in general depend on soil C and nutrient supply. Both soxB and 16S rRNA gene abundances were significantly correlated with the oxidation rate of elemental S (P < 0.05). In addition, more than 80% of the variation in the oxidation rate of elemental S could be explained by the combination of soxB or 16S rRNA gene abundances and soil pH, suggesting that pH not only affected bacterial abundances but also their activity during elemental S oxidation. Clone libraries constructed with the soxB primers showed genera belonging to Alphaproteobacteria, Betaproteobacteria and Deltaproteobacteria and Actinobacteria. The phylogenetic diversity and relative distribution of soxB clones revealed great differences across soils. However, no direct linkage was found between the diversity of S-oxidising bacteria and elemental S oxidation rate.     

Effect of <Emphasis Type="Italic">Silene vulgaris</Emphasis> and Heavy Metal Pollution on Soil Microbial Diversity in Long-Term Contaminated Soil

In this study, we analysed the impact of heavy metals and plant rhizodeposition on the structure of indigenous microbial communities in rhizosphere and bulk soil that had been exposed to heavy metals for more than 150 years. Samples of the rhizosphere of Silene vulgaris and non-rhizosphere soils 250 and 450 m from the source of emission that had different metal concentrations were collected for analyses. The results showed that soils were collected 250 m from the smelter had a higher number of Cd-resistant CFU compared with the samples that were collected from 450 m, but no significant differences were observed in the number of total and oligotrophic CFU or the equivalent cell numbers between rhizosphere and non-rhizosphere soils that were taken 250 and 450 m from the emitter. Unweighted pair group method with arithmetic mean (UPGMA) cluster analysis of the denaturing gradient gel electrophoresis (DGGE) profiles, as well as a cluster analysis that was generated on the phospholipid fatty acid (PLFA) profiles, showed that the bacterial community structure of rhizosphere soils depended more on the plant than on the distance and metal concentrations. The sequencing of the 16S rDNA fragments that were excised from the DGGE gel revealed representatives of the phyla Bacteroidetes, Acidobacteria, Gemmatimonadetes, Actinobacteria and Betaproteobacteria in the analysed soil with a predominance of the first three groups. The obtained results demonstrated that the presence of S. vulgaris did not affect the number of CFUs, except for those of Cd-resistant bacteria. However, the presence of S. vulgaris altered the soil bacterial community structure, regardless of the sampling site, which supported the thesis that plants have a higher impact on soil microbial community than metal contamination.     

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.     

Distinct effect of nitrogen fertilisation and soil depth on nitrous oxide emissions and nitrifiers and denitrifiers abundance

The nitrous oxide and molecular N emissions from 5-cm length subsamples taken from 20-cm length sample corers containing eutric Cambisol soil fertilised either with urea, ammonium or nitrate for 1 year have been examined using gas chromatography. At the beginning of the incubation, the same N rate (260 kg N/ha) was added to the soil and kept constant during the experiment. The total abundance of the soil Bacteria and Archaea and that of nitrifiers and denitrifiers was estimated by quantitative PCR of the corresponding biotic variables 16S rRNA, amoA and napA, narG, nirK, nirS, norB, nosZI and nosZII genes. The abiotic variables dissolved oxygen, pH, exchangeable NH₄⁺-N and NO₃^?-N contents and total C and total N were also analysed. None of the three fertilisers affected the total abundance of Bacteria and Archaea and nitrification was the main driver of nitrous oxide production in the 0- to 5-cm and 5- to 10-cm soil layers while denitrification was in the 10- to 15-cm and 15- to 20-cm soil horizons. Parallel to the reduction in the content of dissolved oxygen along the soil profile, there was a decrease in the total and relative abundance of the bacterial and archaeal amoA gene and an increase in the abundances of the denitrification genes, mainly in the 10- to 15-cm and 15- to 20-cm soil layers. A non-metric multidimensional scaling plot comparing the biotic and abiotic variables examined in each of the four 5-cm soil subsamples and the whole 20-cm sample showed a disparate effect of N fertilisation on N gas emissions and abundance of nitrifiers and denitrifiers bacterial and archaeal communities.     

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.     

Influence of Physicochemical Factors on Bacterial Communities Along the Lower Mekong River Assessed by Illumina Next-Generation Sequencing

The relationship between land use and microbial community structure at seven sites along the Lower Mekong River, between Thailand and the Loa People’s Democratic Republic, was investigated using Illumina next-generation sequencing of the V5–V6 hypervariable regions of the 16S rRNA gene. In total, 14,470 operational taxonomic units (OTUs) were observed. Community composition was significantly different between sampling years. Moraxellaceae and Comamonadaceae were the predominant bacterial families in upstream sites, which included agricultural and urban areas in the Loei and Nong Khai provinces of Thailand. Members of the family Comamonadaceae were prevalent in agricultural and urban sites in Bueng Kan Province, while Moraxellaceae and Burkholderiaceae were the major families in a site downstream of an urban area in the Nakhon Phanom Province of Thailand. The bacterial community observed from a forested area of Patam National Park in Thailand showed greatest diversity, and several major bacterial families including Comamonadaceae, Moraxellaceae, and Pseudomonadaceae were more dominant than other sites. The diversity of fecal indicator bacteria, determined by ERIC-PCR DNA fingerprinting, indicated the presence of 29 strains of Escherichia coli and 21 strains of Enterococcus, while TP-RAPD patterns represented six species of Enterococcus. Results of this study indicated that although the difference in the distribution of bacterial phyla and families was found among sampling sites, the bacterial community composition, based on the presence of OTUs, continuously retained its signature across approximately 758 km along the Lower Mekong River, regardless of the type of land use. Water parameters, including temperature, turbidity, DO, and air temperature, also differentially affected the abundance of bacterial families along the Mekong River.     

Bacterivore nematodes stimulate soil gross N transformation rates depending on their species

We conducted a microcosm experiment with soil being sterilized, reinoculated with native microbial community and subsequently manipulated the bacterivorous nematodes, including three treatments: without (CK) or with introducing one species of the two bacterivores characterized with different body size but similar c-p (colonizer-persister) value (Rhabditis intermedia and Protorhabditis oxyuroides, accounted for 6 and 59% of bacterivores in initially undisturbed soil, respectively). We monitored the N₂O and CO₂ emissions, soil properties, and especially quantified gross N transformation rates using ¹⁵N tracing technique after the 50 days incubation. No significant differences were observed on soil NH₄ ⁺ and NO₃ ^? concentrations between the CK and two bacterivores, but this was not the case for gross N transformation rates. In comparison to CK, R. intermedia did not affect soil N transformation rates, while P. oxyuroides significantly increased the rates of mineralization of organic N to NH₄ ⁺, oxidation of NH₄ ⁺ to NO₃ ^?, immobilization of NO₃ ^? to organic N and dissimilatory NO₃ ^? reduction to NH₄ ⁺. Furthermore, the mean residence time of NH₄ ⁺ and NO₃ ^? pool was greatly lowered by P. oxyuroides, suggesting it stimulated soil N turnover. Such stimulatory effect was unrelated to the changes in abundance of bacteria and ammonia-oxidizing bacteria (AOB). In contrast to CK, only P. oxyuroides significantly promoted soil N₂O and CO₂ emissions. Noticeably, bacterivores increased the mineralization of recalcitrant organic N but decreased soil δ¹³C_-TOC and δ¹⁵N_-TN values, in particular for P. oxyuroides. Combining trait-based approach and isotope-based analysis showed high potential in moving forward to a mechanistic understanding of bacterivore-mediated N cycling.     

Responses of soil nitrous oxide production and abundances and composition of associated microbial communities to nitrogen and water amendment

Soil moisture and nitrogen (N) are two important factors influencing N₂O emissions and the growth of microorganisms. Here, we carried out a microcosm experiment to evaluate effects of soil moisture level and N fertilizer type on N₂O emissions and abundances and composition of associated microbial communities in the two typical arable soils. The abundances and community composition of functional microbes involved in nitrification and denitrification were determined via quantitative PCR (qPCR) and terminal restriction length fragment polymorphism (T-RFLP), respectively. Results showed that N₂O production was higher at 90% water-filled pore (WFPS) than at 50% WFPS. The N₂O emissions in the two soils amended with ammonium were higher than those amended with nitrate, especially at relatively high moisture level. In both soils, increased soil moisture stimulated the growth of ammonia-oxidizing bacteria (AOB) and nitrite reducer (nirK). Ammonium fertilizer treatment increased the population size of AOB and nirK genes in the alluvial soil, while reduced the abundances of ammonia-oxidizing archaea (AOA) and denitrifiers (nirK and nosZ) in the red soil. Nitrate addition had a negative effect on AOA abundance in the red soil. Total N₂O emissions were positively correlated to AOB abundance, but not to other functional genes in the two soils. Changed soil moisture significantly affected AOA rather than AOB community composition in both soils. The way and extent of N fertilizers impacted on nitrifier and denitrifier community composition varied with N form and soil type. These results indicate that N₂O emissions and the succession of nitrifying and denitrifying communities are selectively affected by soil moisture and N fertilizer form in the two contrasting types of soil.     

Bacterial Community Composition and Genes for Herbicide Degradation in a Stormwater Wetland Collecting Herbicide Runoff

Stormwater wetlands collect and attenuate runoff-related herbicides, limiting their transport into aquatic ecosystems. Knowledge on wetland bacterial communities with respect to herbicide dissipation is scarce. Previous studies showed that hydrological and hydrochemical conditions, including pesticide removal capacity, may change from spring to summer in stormwater wetlands. We hypothesized that these changes alter bacterial communities, which, in turn, influence pesticide degradation capacities in stormwater wetland. Here, we report on bacterial community changes in a stormwater wetland exposed to pesticide runoff, and the occurrence of trz, atz, puh, and phn genes potentially involved in the biodegradation of simazine, diuron, and glyphosate. Based on T-RFLP analysis of amplified 16S rRNA genes, a response of bacterial communities to pesticide exposure was not detected. Changes in stormwater wetland bacterial community mainly followed seasonal variations in the wetland. Hydrological and hydrochemical fluctuations and vegetation development in the wetland presumably contributed to prevent detection of effects of pesticide exposure on overall bacterial community. End point PCR assays for trz, atz, phn, and puh genes associated with herbicide degradation were positive for several environmental samples, which suggest that microbial degradation contributes to pesticide dissipation. However, a correlation of corresponding genes with herbicide concentrations could not be detected. Overall, this study represents a first step to identify changes in bacterial community associated with the presence of pesticides and their degradation in stormwater wetland.     

Taxon-specific responses of soil microbial communities to different soil priming effects induced by addition of plant residues and their biochars

Purpose

This work investigated changes in priming effects and the taxonomy of soil microbial communities after being amended with plant feedstock and its corresponding biochar.

Materials and methods

A soil incubation was conducted for 180 days to monitor the mineralization and evolution of soil-primed C after addition of maize and its biochar pyrolysed at 450 °C. Responses of individual microbial taxa were identified and compared using the next-generation sequencing method.

Results and discussion

Cumulative CO₂ showed similar trends but different magnitudes in soil supplied with feedstock and its biochar. Feedstock addition resulted in a positive priming effect of 1999 mg C kg^?1 soil (+253.7 %) while biochar gave negative primed C of ?872.1 mg C kg^?1 soil (?254.3 %). Linear relationships between mineralized material and mineralized soil C were detected. Most priming occurred in the first 15 days, indicating co-metabolism. Differences in priming may be explained by differences in properties of plant material, especially the water-extractable organic C. Predominant phyla were affiliated to Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Firmicutes, Planctomycetes, Proteobacteria, Verrucomicrobia, Ascomycota, Basidiomycota, Blastocladiomycota, Chytridiomycota, Zygomycota, Euryarchaeota, and Thaumarchaeota during decomposition. Cluster analysis resulted in separate phylogenetic grouping of feedstock and biochar. Bacteria (Acidobacteria, Firmicutes, Gemmatimonadetes, Planctomycetes), fungi (Ascomycota), and archaea (Euryarchaeota) were closely correlated to primed soil C (R ²?=??0.98, ?0.99, 0.84, 0.81, 0.91, and 0.91, respectively).

Conclusions

Quality of plant materials (especially labile C) shifted microbial community (specific microbial taxa) responses, resulting in a distinctive priming intensity, giving a better understanding of the functional role of soil microbial community as an important driver of priming effect.

     

Effect of P stoichiometry on the abundance of nitrogen-cycle genes in phosphorus-limited paddy soil

Previous studies have shown that phosphorus addition to P-limited soils increases gaseous N loss. A possible explanation for this phenomenon is element stoichiometry (specifically of C:N:P) modifying linked nutrient cycling, leading to enhanced nitrification and denitrification. In this study, we investigated how P stoichiometry influenced the dynamics of soil N-cycle functional genes. Rice seedlings were planted in P-poor soils and incubated with or without P application. Quantitative PCR was then applied to analyze the abundance of ammonia-oxidizing (amoA) and denitrifying (narG nirK, nirS, nosZ) genes in soil. P addition reduced bacterial amoA abundance but increased denitrifying gene abundance. We suggest this outcome is due to P-induced shifts in soil C:P and N:P ratios that limited ammonia oxidization while enhancing P availability for denitrification. Under P application, the rhizosphere effect raised ammonia-oxidizing bacterial abundance (amoA gene) and reduced nirK, nirS, and nosZ in rhizosphere soils. The change likely occurred through greater C input and O₂ release from roots, thus altering C availability and redox conditions for microbes. Our results show that P application enhances gaseous N loss potential in paddy fields mainly through stimulating denitrifier growth. We conclude that nutrient availability and elemental stoichiometry are important in regulating microbial gene responses, thereby influencing key ecosystem processes such as denitrification.

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Graphical abstract ?

     

Application of compost and clay under water-stressed conditions influences functional diversity of rhizosphere bacteria

Applications of compost and clay to ameliorate soil constraints such as water stress are potential management strategies for sandy agricultural soils. Water repellent sandy soils in rain-fed agricultural systems limit production and have negative environmental effects associated with leaching and soil erosion. The aim was to determine whether compost and clay amendments in a sandy agricultural soil influenced the rhizosphere microbiome of Trifolium subterraneum under differing water regimes. Soil was amended with compost (2% w/w), clay (5% w/w) and a combination of both, in a glasshouse experiment with well-watered and water-stressed (70 and 35% field capacity) treatments. Ion Torrent 16S rRNA sequencing and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis of functional gene prediction were used to characterise the rhizosphere bacterial community and its functional component involved in nitrogen (N) cycling and soil carbon (C) degradation. Compost soil treatments increased the relative abundance of copiotrophic bacteria, decreased labile C and increased the abundance of recalcitrant C degrading genes. Predicted N cycling genes increased with the addition of clay (N₂ fixation, nitrification, denitrification) and compost + clay (N₂ fixation, denitrification) and decreased with compost (for denitrification) amendment. Water stress did not alter the relative abundance of phylum level taxa in the presence of compost, although copiotrophic Actinobacteria increased in relative abundance with addition of clay and with compost + clay. A significant role of compost and clay under water stress in influencing the composition of rhizosphere bacteria and their implications for N cycling and C degradation was demonstrated.