The foliar spray of <Emphasis Type="Italic">Rhodopseudomonas palustris</Emphasis> grown under <Emphasis Type="Italic">Stevia</Emphasis> residue extract promotes plant growth via changing soil microbial community

Purpose

The extract of Stevia residue is an ideal substitute for cultivation of the purple nonsulfur bacterium, like Rhodopseudomonas palustris (R. palustris). But the influence of R. palustris grown under residue extract on its downstream application is still not well-characterized. The objective of this study was to assess the effect of foliar spray of R. palustris grown under Stevia residue extract on the plant growth and soil microbial properties.

Materials and methods

A pot experiment was carried out under the greenhouse condition, consisting of four treatments varying in the sprayed substances: sterilized water (control), R. palustris grown under the chemical medium supplemented with L-tryptophan (SyT), R. palustris grown under Stevia residue extract supplemented with L-tryptophan (ExT), and R. palustris grown under Stevia residue extract supplemented with NH₄Cl (ExT). The net photosynthesis rate of the uppermost leaves was measured with a portable photosynthesis system. Soil microbial activity was analyzed by microcalorimetry. Soil bacterial community components were determined by real-time quantitative PCR (qPCR) and high-throughput sequencing techniques.

Results and discussion

Compared with SyT, the R. palustris grown under Stevia residue extract not only improved the plant biomass and the net photosynthetic rate to a large extent, but also increased soil microbial metabolic activity and altered community compositions as well. The treatments receiving R. palustris, especially ExT and ExN, increased the relative abundances of some functional guilds involved in C turnover and nutrient cycling in soil, including Acidobacteria, Actinobacteria, Proteobacteria, Gemmatimonadaetes, Nitrospirae, and Planctomycetes.

Conclusions

R. palustris grown under the Stevia residue extract showed advantages over that under the chemical medium on both plant growth and soil microbial properties. One of the possible reasons could result from the increases in microbial activity and several bacterial keystone guilds involved into C and nutrient cycling, both of which potentially contribute to the improved plant growth. The results would be conducive to the downstream application of R. palustris in an economical way.

     

Effect of Biofumigants on Soil Microbial Communities and Ecotoxicology of Earthworms (<Emphasis Type="Italic">Eisenia andrei</Emphasis>)

Biofumigation is considered a good alternative to chemical fumigation because it can control crop pathogens and diseases with lower health and environmental risks than chemical fumigants. Glucosinolates are volatile compounds found in most Brassica species, and when hydrolysed, it forms a range of natural toxins including isothiocyanates that act as biofumigants. However, the effect of glucosinolates and their breakdown products on non-target and beneficial soil organisms is not well documented. Three biofumigants, broccoli, mustard and oilseed radish, were evaluated for their effect on earthworms (Eisenia andrei) and the soil microbial community. Sub-lethal endpoints, including growth and reproductive success of the earthworms, were monitored. Genotoxicity of the biofumigants towards earthworms was evaluated by means of the comet assay. Broccoli reduced earthworm reproduction while mustard induced more DNA strand breaks in earthworm cells compared to the control. Soil microbial community function and structure were evaluated by means of community level physiological profiling and phospholipid fatty acid analyses. The effects exerted by the biofumigants on the microbial community were the most pronounced within the first 14 days after application. Carbon substrate utilisation was most affected by the oilseed radish treatment and microbial community structure by the mustard treatment.     

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.     

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.

     

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.     

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.     

<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.     

Long-term fertilisation regimes affect the composition of the alkaline phosphomonoesterase encoding microbial community of a vertisol and its derivative soil fractions

Alkaline phosphomonoesterase (ALP) mainly originates from soil microbial secretion and plays a crucial role in the turnover of soil phosphorus (P). To examine the response of ALP-encoding microbial communities (analysed for the biomarker of the ALP gene, phoD) of soils and derivative soil fractions to different fertilisation regimes, soil samples were collected from a long-term experimental field (over 35 years). The different organic P (Po) pools of soil fractions and the ALP activity of soil were also determined. Compared with chemical-only fertilised soils, the ALP activity was 232–815% higher in organic-amended soils, and the highest enzyme activity was observed in the organic-only fertilised treatment. The abundance of the phoD gene harbouring in soil fractions, determined by quantitative PCR (qPCR), was affected by different fertilisations. The highest abundance of the phoD gene was generally detected in the 2–63-μm-sized fraction (silt), but most phoD-encoding microbial species were associated to the 0.1–2-μm-sized fraction (clay) in the chemical-only fertilised soil. The contents of labile Po (LPo), moderately labile Po (MLPo) and fulvic acid-associated Po (FAPo) were significantly correlated with the phoD gene abundance, whereas only LPo content was significantly correlated with the ALP activity. The dominant phoD-encoding phylas were Actinobacteria and Proteobacteria, according to a high-throughput sequencing. Bradyrhizobium, a N₂-fixer identified as a phoD-encoding genus, showed the highest abundance in fertilised soils. The abundance of Bradyrhizobium, Streptomyces, Modestobacter, Lysobacter, Frankia and Burkholderia increased with the organic-only amendment and was significantly correlated with the ALP activity. According to structure equation models (SEM), pH and LPo content significantly and directly affected the ALP activity; the soil organic C (C_org) content was related to composition and abundances of phoD-harbouring microbial communities; since both microbial properties were correlated to the ALP activity, the C_org content was indirectly related to the ALP activity. In conclusion, soil management practices can be used to optimise the contents of soil available P and the organic P with regulation of soil ALP activity and the community composition of corresponding microbes.     

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.     

<Emphasis Type="Italic">p</Emphasis>-Coumaric can alter the composition of cucumber rhizosphere microbial communities and induce negative plant-microbial interactions

Phenolics from root exudates or decaying residues are usually referred as autotoxins of several plant species. However, how phenolics affect soil microbial communities and their functional significances are poorly understood. Rhizosphere bacterial and fungal communities from cucumber (Cucumis sativus L.) seedlings treated with p-coumaric acid, an autotoxin of cucumber, were analyzed by high-throughput sequencing of 16S rRNA gene and internal transcribed spacer amplicons. Then, feedback effects of the rhizosphere biota on cucumber seedlings were evaluated by inoculating non-sterilized and sterilized rhizosphere soils to sterilized background soils. p-Coumaric acid decreased the bacterial diversity of rhizosphere but increased fungal diversity and altered the compositions of both the bacterial and fungal communities. p-Coumaric acid increased the relative abundances of microbial taxa with phenol-degrading capability (such as Chaetomium, Humicola, and Mortierella spp.) and microbial taxa which contained plant pathogens (such as Fusarium spp.). However, p-coumaric acid inhibited the relative abundances of Lysobacter, Haliangium, and Gymnoascus spp., whose species can have pathogen-antagonistic and/or plant-growth-promoting effects. The positive effect of cucumber rhizosphere microbiota on cucumber seedling growth was reduced by p-coumaric acid. Overall, our results showed that, besides its direct phytotoxicity, p-coumaric acid can inhibit cucumber seedling growth through generating negative plant-soil microbial interactions.     

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.     

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.     

Long-term and legacy effects of manure application on soil microbial community composition

We analyzed soil prokaryotic and fungal community composition in soils with varying histories of cattle manure application. The manure treatments were (i) annual application for 43 years (MF), (ii) annual application for 14 years followed by 29 years without application (MF14), and (iii) annual application for 30 years followed by 13 years without application (MF30). An annual application of chemical nitrogen (N) fertilizer (CNF) and a non-amended control (Con) were also included. Soil prokaryotic evenness and diversity significantly decreased in MF relative to other treatments in fall, but were similar to the other fertilizer treatments in spring and summer. Distinct prokaryotic and fungal community composition was observed in MF compared to other treatments across fall, spring, and summer seasons. The MF treatment significantly increased the relative abundance of Firmicutes, Gammaproteobacteria, and Gemmatimonadetes, but significantly decreased the relative abundance of Acidobacteria. In fall, the soil prokaryotic and fungal community composition with MF30 was significantly different than the other fertilization treatments. Overall, the study showed that annual manure application (MF) led to a different microbial community composition than the other fertilizer treatments. Soil without manure application for 13 years (MF30) had a significantly different microbial community composition from other fertilizer treatments in fall, while the soil without manure application for 29 years (MF14) resembled a microbial community that had never received manure.     

Assessment of <Emphasis Type="Italic">Koelreuteria paniculata</Emphasis> Seedling for Phytroremediation of Pyrene-Contaminated Soils

Phytoremediation is a cost-effective and environmentally friendly technology using plants for the cleanup of both inorganic and organic contaminated sites. In this study, a pot culture experiment has been conducted for 180 days in a greenhouse to examine the capability of Koelreuteria paniculata on pyrene (Pyr) dissipation in contaminated soil. Three treatments were employed and they were: (1) polluted soil with K. paniculata fine roots addition (T1), (2) polluted soil with planted seedlings (T2), and (3) polluted soil (C). Results showed Pyr concentration in soils was reduced by 21.4, 36.2, and 86.4% by natural losses, fine roots addition, and planted K. paniculata treatments, respectively, meaning plants substantially enhanced the dissipation of Pyr from soil. Cultivated K. paniculata seedlings significantly increased soil total nitrogen (TN), total organic carbon, dissolved organic carbon (DOC), and microbial biomass carbon, but not total phosphorus, when compared to the control. The removal efficiency of Pyr was lower in the adding of fine roots treatment than in the planted K. paniculata treatment. The principal component analysis indicated the promotional dissipation of Pyr in soil by planted K. paniculata was likely attributed to increased microbial quantity and activity, DOC, and TN content in the rhizosphere. Our results suggest that K. paniculata is a suitable plant species used in phytoremediation for Pyr-contaminated soils and the efficiency on the dissipation of Pyr is considerably enhanced using living plants than adding dead organic matters. The study provided a reference for the application of K. paniculata in the remediation of Pyr-contaminated soil.     

Geographic distance and amorphous iron affect the abundance and distribution of <Emphasis Type="Italic">Geobacteraceae</Emphasis> in paddy soils in China

Purpose

Geobacteraceae are important dissimilatory Fe (III)-reducing microorganisms, influencing the cycling of metals, nutrients as well as the degradation of organic contaminants. However, little is known about their distribution, diversity, and abundance of Geobacteraceae and the effects of environment factors and geographic distance on the distribution and diversity of Geobacteraceae in paddy soils remain unclear. Therefore, the objectives of this study were to investigate the distribution, diversity, and abundance of Geobacteraceae in paddy soils and to determine key factors in shaping the Geobacteraceae distribution, environmental factors, geographic distance, or both and to quantify their contribution to Geobacteraceae variation.

Materials and methods

Illumina sequencing and quantitative real-time PCR using a primer set targeting 16S rRNA genes of bacteria affiliated with the family Geobacteraceae were employed to measure the community composition, diversity, and abundance patterns of 16S rRNA genes of Geobacteraceae in 16 samples collected from north to south of China. MRT, Mantel test, and VPA were used to analyze the relationship between communities of Geobacteraceae and environmental factors and geographic distance.

Results and discussion

Quantitative PCR showed that the abundance of 16S rRNA genes of Geobacteraceae ranged from (1.20?±?0.18)?×?10⁸ to 1.13?×?10⁹?±?2.25?×?10⁸ copies per gram of soil (dry weight) across different types of soils. Illumina sequencing results showed Geobacter was the dominant genus within the family of Geobacteraceae. Multivariate regression tree (MRT) analysis showed that soil amorphous iron contributed more (22.46 %) to the variation of dominant species of Geobacteraceae than other examined soil chemical factors such as pH (14.52 %), ammonium (5.12 %), and dissolved organic carbon (4.74 %). Additionally, more geographically distant sites harbored less similar communities. Variance partitioning analysis (VPA) showed that geographic distance contributed more to the variation of Geobacteraceae than any other factor, although the environmental factors explained more variation when combined. So, we detected the uneven distribution of Geobacteraceae in paddy soils of China and demonstrated that Geobacteraceae community composition was strongly associated with geographic distance and soil chemical factors including aFe, pH, Fe, DOC, C:N, and NO₃ ^?-N. These results greatly expand the knowledge of the distribution of Geobacteraceae in environments, particularly in terrestrial ecosystems.

Conclusions

Our results showed that geographic distance and amorphous iron played important roles in shaping Geobacteraceae community composition and revealed that both geographic distance and soil properties governed Geobacteraceae biogeography in paddy soils. Our findings will be critical in facilitating the prediction of element cycling by incorporating information on functional microbial communities into current biogeochemical models.

     

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.

     

Changes in methane emission and methanogenic and methanotrophic communities in restored wetland with introduction of <Emphasis Type="Italic">Alnus trabeculosa</Emphasis>

Purpose

The dynamics and uncertainties in wetland methane budgets affected by the introduction of Alnus trabeculosa H. necessitate research on production of methane by methanogenic archaea and consumption by methane-oxidizing microorganisms simultaneously.

Materials and methods

This study investigated methane emission in situ by the closed chamber method, and methanogenic and methanotrophic communities using denatured gradient gel electrophoresis (DGGE) and quantitative PCR based on mcrA (methyl coenzyme M reductase), pmoA (particulate methane monooxygenase) genes in the rhizosphere and non-rhizosphere soils in the indigenous pure Phragmites australis T., and A. trabeculosa–P. australis mixed communities in Chongxi wetland.

Results and discussion

Methane flux rate from the pure P. australis community was 2.4 times larger than that of A. trabeculosa–P. australis mixed community in the rhizosphere and 1.7 times larger in the non-rhizosphere, respectively. The abundance of methanogens was lower in the mixed community soils (3.56?×?10³–6.90?×?10³ copies g^?1 dry soil) compared with the P. australis community (1.47?×?10⁴–1.89?×?10⁴ copies g^?1 dry soil), whereas the methanotrophs showed an opposite trend (2.08?×?10⁶–1.39?×?10⁶ copies g^?1 dry soil for P. australis and 6.20?×?10⁶–1.99?×?10⁶ copies g^?1 dry soil for mixed community soil). A liner relationship between methane emission rates against pmoA/mcrA ratios (R ²?=?0.5818, p?<?0.05, n?=?15) was observed. The community structures of the methane-cycling microorganism based on mcrA and pmoA suggested that acetoclastic methanogens belonging to Methanosarcinaceae and a particular type II methanotroph, Methylocystis, were dominant in these two plant communities.

Conclusions

The introduction of A. trabeculosa would promote the proliferation of methanotrophs, especially the dominant Methylocystis, but not methanogens, ultimately diminishing methane emission in the wetland.

     

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.     

Abundance of transcripts of functional gene reflects the inverse relationship between CH<Subscript>4</Subscript> and N<Subscript>2</Subscript>O emissions during mid-season drainage in acidic paddy soil

Agricultural management significantly affects methane (CH₄) and nitrous oxide (N₂O) emissions from paddy fields. However, little is known about the underlying microbiological mechanism. Field experiment was conducted to investigate the effect of the water regime and straw incorporation on CH₄ and N₂O emissions and soil properties. Quantitative PCR was applied to measure the abundance of soil methanogens, methane-oxidising bacteria, nitrifiers, and denitrifiers according to DNA and mRNA expression levels of microbial genes, including mcrA, pmoA, amoA, and nirK/nirS/nosZ. Field trials showed that the CH₄ and N₂O flux rates were negatively correlated with each other, and N₂O emissions were far lower than CH₄ emissions. Drainage and straw incorporation affected functional gene abundance through altered soil environment. The present (DNA-level) gene abundances of amoA, nosZ, and mcrA were higher with straw incorporation than those without straw incorporation, and they were positively correlated with high concentrations of soil exchangeable NH₄⁺ and dissolved organic carbon. The active (mRNA-level) gene abundance of mcrA was lower in the drainage treatment than in continuous flooding, which was negatively correlated with soil redox potential (Eh). The CH₄ flux rate was significantly and positively correlated with active mcrA abundance but negatively correlated with Eh. The N₂O flux rate was significantly and positively correlated with present and active nirS abundance and positively correlated with soil Eh. Thus, we demonstrated that active gene abundance, such as of mcrA for CH₄ and nirS for N₂O, reflects the contradictory relationship between CH₄ and N₂O emissions regulated by soil Eh in acidic paddy soils.     

Microbial inoculation of seeds characteristically shapes the rhizosphere microbiome in <Emphasis Type="Italic">desi</Emphasis> and <Emphasis Type="Italic">kabuli</Emphasis> chickpea types

Purpose

Chickpea is generally cultivated after seed treatment with host-specific Mesorhizobium ciceri, the nitrogen-fixing bacterium forming root nodules. Some species of free-living cyanobacteria are capable of nitrogen fixation. We examined the rhizosphere microbiota changes and the potential for plant growth promotion by applying a free-living, nitrogen-fixing cyanobacterium and the biofilm formulation of cyanobacterium with M. ciceri, relative to M. ciceri applied singly, to two each of desi and kabuli varieties of chickpea.

Materials and methods

Denaturing gradient gel electrophoresis (DGGE) profiles of archaeal, bacterial and cyanobacterial communities and those of phospholipid fatty acids (PLFAs) were obtained to evaluate the changes of the microbial communities in the chickpea rhizosphere. Plant growth attributes, including the pod yields and the availabilities of soil macronutrients and micronutrients, were monitored.

Results and discussion

The DGGE profiles showed distinct and characteristic changes due to the microbial inoculation; varietal differences exerted a marked influence on the archaeal and cyanobacterial communities. However, bacterial communities were modulated more by the type of microbial inoculants. Abundance of Gram-negative bacteria (in terms of notional PLFAs) differed between the desi and the kabuli varieties inoculated with M. ciceri alone, and the principal component analysis of PLFA profiles confirmed the characteristic effect of microbial inoculants tested. Microbial inoculation led to increases in the 100-seed weight and differential effects on the concentrations of available nitrogen and phosphorus, and those of iron, zinc and copper, suggesting their increased cycling in the rhizosphere.

Conclusions

Microbial inoculation of chickpea brought out the characteristic changes in rhizosphere microbiota. Consequently, the growth promotion of chickpea and nutrient cycling in its rhizosphere distinctively differed. Further studies are needed to analyse the association and dynamic changes in the microbial communities to define the subset of microorganisms selected by chickpea in its rhizosphere and the influence of microbial inoculation.