Responses of soil phosphorus pools accompanied with carbon composition and microorganism changes to phosphorus-input reduction in paddy soils

In rice-wheat rotation systems, changes in soil phosphorus(P) pools and microorganisms in rice-growing seasons have been studied;however, further investigations are required to test whether these indexes exhibit different responses in wheat-growing seasons. Additionally, such studies need to include potential variations in soil carbon(C) structure and microbial community composition. In this study, a long-term rice-wheat rotation P-input reduction experiment was conducted to observe the variations in soil P pools and C composition in the 7th wheat season and to investigate the responses of soil enzyme activity and microbial communities. Four P fertilization treatments were included in the experiment, i.e., P application for rice season only(PR), for wheat season only(PW), and for both rice and wheat seasons(PR+W) and no P application in either season(Pzero). Compared with PR+W treatment, Pzero treatment significantly decreased(P < 0.05) labile and stable P pools. Different P fertilization regimes altered soil microbial community composition and enzyme activity, whereas C composition did not vary. However, PW treatment resulted in relatively more O-alkyl-C than PR treatment and the highest number of microorganisms. Besides, the higher ratios of fungi/bacteria and Gram-positive bactetia/Gram-negative bactetia were related to labile C pools, particularly O-alkyl-C, as opposed to recalcitrant C. Our results clarified the status of soil P pools, C chemistry, and the response of microorganisms under dry-farming conditions in the P input-reduced rice-wheat rotation system.     

Effect of lead on growth characteristics of microorganisms in soil and rhizosphere of Dactylis glomerata

The effects of lead oxide and lead nitrate on the growth strategies of microbial communities in the soil and in the rhizosphere of orchard grass (Dactylis glomerata L.) were studied. The maximum specific growth rate of the microorganisms (μ_m) changed significantly when the concentration of mobile forms of lead in the soil exceeded 170 mg Pb/kg, which corresponded to the addition of 400–1000 mg Pb/kg of soil in the form of lead nitrate. The addition of lead resulted in the suppression of a part of the r-strategists and in the more active development of the K-strategists in the adapted microbial community. It was demonstrated that the community of rhizosphere microorganisms could be a more sensitive indicator of lead pollution than the nonrhizosphere microbial community. The values of the auxotrophy index (the ratio between the μ_m values upon the growth on glucose and yeast extract) demonstrated a tendency towards a decrease in the metabolic diversity of the soil microbial community under the impact of lead.     

Effects of modified Pb-, Zn-, and Cd- availability on the microbial communities and on the degradation of isoproturon in a heavy metal contaminated soil

The effects of modified heavy metal (HM) availability on the microbial community structure and on the microbe-mediated degradation of herbicide isoproturon (IPU) were evaluated in soil with a long-term HM contamination. The fate of ¹⁴C-ring labelled IPU was investigated for over 60 days under controlled microcosm conditions. Phosphate mineral apatite and a water solution of Pb, Zn, and Cd salts were previously homogeneously mixed into the soil material to reduce and to increase the proportion of bioavailable HM, respectively. The availability of Pb, Zn, and Cd was determined by HM fractionation and plant uptake 110 days after the addition of amendments, shortly before IPU addition. Apatite treatment reduced the availability of HM, but did not affect the microbial biomass and the microbial community structure on the genotype level (total soil DNA-RAPD). However, it changed the microbial community structure on the phenotype level, based on the composition of phospholipid fatty acids (PLFA) at the end of the degradation experiment. The degradation of IPU did not change. In contrast to apatite treatment, HM supplementation increased the bioavailability of Pb, Zn and Cd, which resulted in biomass reduction and changes of microbial community structure on the genotypic (total soil DNA-RAPD) and phenotypic (PLFA) level. Increased bioavailability of HM also significantly reduced the rate of IPU degradation and mineralisation. The total mineralisation over a period of 60 days decreased from 12 to 5% of initial ¹⁴C. Increased HM bioavailability did not influence the degradation pathways and kinetics of IPU.     

Dynamics of the methanogenic archaeal community in anoxic rice soil upon addition of straw

Addition of rice straw, which is a common practice in rice agriculture, generally results in enhanced production and emission of the greenhouse gas methane (CH₄). However, it is unclear whether straw addition affects only the activity or also the composition of the methanogenic microbial community. It is also unclear to what extent methanogenic archaea would be able to proliferate in the soil. Anoxic slurries of Italian rice‐field soil produced CH₄ after a lag, during which ferric iron and sulfate were reduced. Addition of rice straw slightly decreased this lag and greatly enhanced the subsequent production of CH₄. At the same time, addition of rice straw enhanced the intermediate production of H₂ and acetate that served as the methanogenic substrates. Compared with the unamended control, the addition of rice straw resulted in an increased concentration of phospholipid fatty acids in the soil. Quantitative ‘real‐time’ PCR targeting the 16S rRNA gene also showed increased copy numbers of both Bacteria and Archaea in the straw‐amended soil at the end of the experiment. The composition of the archaeal community was followed over time by terminal restriction length polymorphism (T‐RFLP) analysis of the archaeal 16S rRNA genes extracted from straw‐amended soil and the control. Rice Cluster‐I (RC‐I) methanogens and Methanosarcinaceae were the most abundant methanogenic populations, followed by Methanobacteriales, Methanomicrobiales and Methanosaetaceae. Addition of rice straw resulted in a relative increase of Methanosarcinaceae and Methanobacteriales and a relative decrease of RC‐I methanogens and Methanomicrobiales. Our results revealed a dynamic methanogenic community in anoxic rice‐field soil and showed that addition of organic matter selectively enhanced the growth of particular methanogenic populations, which were apparently better adapted to the presence of straw than the others. The extent of archaeal growth was consistent with that expected theoretically from the ambient Gibbs free energies of hydrogenotrophic and acetoclastic methanogenesis.     

Effect of agricultural land use change on community composition of bacteria and ammonia oxidizers

Purpose

Soil microbial communities can be strongly influenced by agricultural practices, but little is known about bacterial community successions as land use changes. The objective of this study was to determine microbial community shifts following major land use changes in order to improve our understanding of land use impacts on microbial community composition and functions.

Materials and methods

Four agricultural land use patterns were selected for the study, including old rice paddy fields (ORP), Magnolia nursery planting (MNP), short-term vegetable (STV), and long-term vegetable (LTV) cultivation. All four systems are located in the same region with same soil parent material (alluvium), and the MNP, STV, and LTV systems had been converted from ORP for 10, 3, and 30 years, respectively. Soil bacteria and ammonia oxidizer community compositions were analyzed by 454 pyrosequencing and terminal restriction fragment length polymorphism, respectively. Quantitative PCR was used to determine 16S rRNA and amoA gene copy numbers.

Results and discussion

The results showed that when land use was changed from rice paddy to upland systems, the relative abundance of Chloroflexi increased whereas Acidobacteria decreased significantly. While LTV induced significant shifts of bacterial composition, MNP had the highest relative abundance of genera GP1, GP2, and GP3, which were mainly related to the development of soil acidity. The community composition of ammonia-oxidizing bacteria (AOB) but not ammonia-oxidizing archaea was strongly impacted by the agricultural land use patterns, with LTV inducing the growth of a single super predominant AOB group. The land use changes also induced significant shifts in the abundance of 16S rRNA and bacterial amoA genes, but no significant differences in the abundance of archaea amoA was detected among the four land use patterns. Soil total phosphorous, available phosphorous, NO₃ ^?, and soil organic carbon contents and pH were the main determinants in driving the composition of both bacteria and AOB communities.

Conclusions

These results clearly show the significant impact of land use change on soil microbial community composition and abundance and this will have major implications on the microbial ecology and nutrient cycling in these systems, some of which is unknown. Further research should be directed to studying the impacts of these microbial community shifts on nutrient dynamics in these agroecosystems so that improved nutrient management systems can be developed.     

Combined amendment of immobilizers and the plant growth-promoting strain Burkholderia phytofirmans PsJN favours plant growth and reduces heavy metal uptake

In the surroundings of a former Pb/Zn smelter in Arnoldstein (Austria) heavy metal concentrations in planted crops exceed thresholds for usage as food and feed. The aim was to study the effects of a plant growth-promoting bacterial strain in combination with immobilizing soil amendments on plant growth, heavy metal uptake and on microbial community structure. Pot experiments were performed whereby two maize cultivars were grown in different contaminated soils and treatments consisted of Burkholderia phytofirmans strain PsJN with and without addition of gravel sludge and siderite bearing material. Inoculation with strain PsJN significantly improved root and shoot biomass of maize independent of immobilizer addition. Analysis of heavy metal content of the rhizosphere and leaves indicated that immobilizing amendments had significant reducing effects on NH₄NO₃ extractable Zn and Pb in soil and in plants grown in treated soils. Microbiomes were analysed by cultivation-independent pyrosequencing analysis of 16S rRNA genes. The results showed clear effects on community composition in response to the immobilizer amendments, whereas inoculation with B. phytofirmans affected microbiome diversity only to a minor extent.     

In vitro studies of the impact of the naked soil amoeba Thecamoeba similis Greef,feeding on phototrophic soil biofilms

The effect of grazing by the naked soil amoeba Thecamoeba similis feeding on algae of in vitro phototrophic soil biofilms was investigated in terms of carbon biomass of algae, bacteria and amoebae and compared to shifts in the microbial community determined by 16S rDNA t-RFLP patterns. In a first approach, grazing of T. similis on unialgal Xanthonema hormidioides biofilms growing on regosol was investigated. The growth rate of T. similis was 0.5 divisions per day and the production efficiency reached 25% (allocation of prey-carbon to predator-carbon). The algal biomass decreased from the original 100% down to 7% at the end of the experiment. The increase of egested residues enhanced bacterial growth; the biomass carbon ratio bacteria vs. algae increased from 0.25 to 4.5 indicating the degradation of the algal biofilm, while the 16S rDNA t-RFLP patterns indicated changes in the composition of the microbial community. A subsequent experiment was conducted by inoculating T. similis on a natural biofilm community consisting of trichomes of cyanobacteria, several species of Chlorophyceae and Xanthophyceae. The total algal biomass (including cyanobacteria) remained constant during the experiment. However, 73% of the algal biomass without cyanobacteria was grazed, while the amount of mucous Chlamydocapsa spec. doubled from 32% to 68%. The growth rate of T. similis was 0.4 divisions per day and the production efficiency was only 13%. The 16S rDNA t-RFLP patterns showed a shift of the microbial community. Our results give a first insight into the obviously high potential of naked soil amoebae feeding on algae to change the structures of both the algal and bacterial communities of phototrophic soil biofilms.     

Transgenic Bt rice does not affect enzyme activities and microbial composition in the rhizosphere during crop development

Use of transgenic crops, including those expressing the insecticidal Cry protein from Bt, is increasing at a rapid rate in worldwide. Field and laboratory studies of transgenic Bt crops have been carried out to detect the persistence and activity of the Cry protein in soil and its effect on soil microorganisms to assess their risks to environment. However, there were few studies that evaluate the seasonal effects of Bt rice on rhizosphere soil microbial communities compared to those of insecticides commonly applied in paddy soil for the control of lepidopteran insects. In this study, seasonal effects of transgenic rice expressing the Cry1Ab insecticidal protein active against lepidoperan pests and the insecticide triazophos [3-(o,o-diethyl)-1-phenyl thiophosphoryl-1,2,4-triazol] on soil enzyme activities and microbial communities were compared under field conditions. During a 2-year field study, rhizosphere soil samples of transgenic-Bt rice (Bt), non-Bt parental rice (Ck) and non-Bt parental rice with triazophos (Ckp) applied were taken at four stages in the rice developmental cycle: seedling, booting, heading and maturing. Microbial processes were investigated by measuring different biochemical activities including those involved in C and P cycling. Denaturing gradient gel electrophoresis (DGGE) and terminal-restriction fragment length polymorphism (T-RFLP) analyses were used to compare rhizosphere microbial compositions. Some occasional and inconsistent effects of the application of triazophos on the bacterial composition in the rhizosphere soil of rice plant were found at the booting and heading stages as compared with that of transgenic-Bt rice. There were no statistically significant differences (P>0.05) in phosphatase activity, dehydrogenase activity, respiration, methanogenesis or fungal community composition in rhizosphere soil between Bt, Ck and Ckp over the rice cropping cycle. However, seasonal variations in the selected enzyme activities and microbial community composition in the rhizosphere soil of Bt, Ck and Ckp were clearly detected. These results suggested that the changes in rhizophere soil microbial community composition associated with the crop growth stage overweighed the application of triazophos and the cry1Ab gene transformation. KMD1 (Bt) rice expressing the cry1Ab gene had no measurable adverse effect on the key microbial processes or microbial community composition in rhizophere soil over 2 years of rice cropping.     

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.     

Long-term impact of fertilization on activity and composition of bacterial communities and metabolic guilds in agricultural soil

To explore long-term impact of organic and inorganic fertilizers on microbial communities, we targeted both the total bacterial community and the autotrophic ammonia oxidizing bacteria (AOB) in soil from six treatments at an experimental field site established in 1956: cattle manure, sewage sludge, Ca(NO₃)₂, (NH₄)₂SO₄, unfertilized and unfertilized without crops. All plots, except the bare fallows, were cropped with maize. Effects on activity were assessed by measuring the basal respiration and substrate induced respiration (SIR) rates, and the potential activity of the AOB. To determine the bacterial community composition, 16S rRNA genes were used to fingerprint total soil communities by terminal restriction fragment length polymorphism analysis and AOB communities by denaturing gradient gel electrophoresis. The fertilization regimes had clear effects on both activity and composition of the soil communities. Basal respiration and r, which was kinetically derived as the exponentially growing fraction of the SIR-response, correlated well with the soil organic C content (r=0.93 and 0.66, respectively). Soil pH ranged from 3.97 to 6.26 in the treatments and was found to be an important factor influencing all microbial activities. pH correlated negatively with the ratio between basal respiration and SIR (r=0.90), indicating a decreased efficiency of heterotrophic microorganisms to convert organic carbon into microbial biomass in the most acid soils with pH 3.97 and 4.68 ((NH₄)₂SO₄ and sewage sludge fertilized plots, respectively). The lowest SIR and ammonia oxidation rates were also found in these treatments. In addition, these treatments exhibited individually different community fingerprints, showing that pH affected the composition of AOB and total bacterial communities. The manure fertilized plots harbored the most diverse AOB community and the pattern was linked to a high potential ammonia oxidation activity. Thus, the AOB community composition appeared to be more strongly linked to the activity than the total bacterial communities were, likely explained by physiological differences in the populations present.     

Effects of phosphorus addition on soil microbial biomass and community composition in three forest types in tropical China

Elevated nitrogen (N) deposition in humid tropical regions may aggravate phosphorus (P) deficiency in forest on old weathered soil found in these regions. From January 2007 to August 2009, we studied the responses of soil microbial biomass and community composition to P addition (in two monthly portions at level of 15 g P m^?2 yr^?1) in three tropical forests in southern China. The forests were an old-growth forest and two disturbed forests (mixed species and pine dominated). The objective was to test the hypothesis that P addition would increase microbial biomass and change the composition of the microbial community, and that the old-growth forests would be more sensitive to P addition due to its higher soil N availability. Microbial biomass C (MBC) was estimated twice a year and the microbial community structure was quantified by phospholipid fatty acid (PLFA) analysis at the end of the experiment. Addition of P significantly increased the microbial biomass and altered the microbial community composition in the old-growth forest, suggesting that P availability is one of the limiting factors for microbial growth. This was also reflected by significant increases in soil respiration after P addition. In contrast, P addition had no effect on the microbial biomass and the microbial community composition in the pine forests. Also in the mixed forest, the microbial biomass did not significantly respond to P addition, but soil respiration and the ratio of fungal-to-bacteria was significantly increased.     

Activity and composition of the methanogenic archaeal community in soil vegetated with wild versus cultivated rice

Wild rice (Oryza rufipogon) is a problematic weed in fields of cultivated rice (Oryza sativa). We hypothesized that the composition and/or the activity of the methanogenic microbial communities might be different in soil grown with cultivated versus wild rice. We used samples from Hainan, China, where wild rice grew on a field adjacent to cultivated rice. The composition of the methanogenic archaeal community was analyzed in samples of rice soil by targeting the 16S rRNA gene. Analysis of the terminal restriction fragment length polymorphism (T-RFLP) showed similar patterns in soil from wild versus cultivated rice. Sequences of archaeal 16S rRNA genes also showed similar composition in soil from wild versus cultivated rice, revealing the presence of Methanosarcinaceae, Methanosaetaceae, Methanobacteriales, Methanocellales (Rice Cluster I), Rice Cluster II, Crenarchaeota Group I.3 and Crenarchaeota Group I.1b. Incubation of soil samples under anoxic conditions generally resulted in vigorous CH₄ production after a lag phase of 7-8 days. Production of CH₄ was partially inhibited by methyl fluoride, a specific inhibitor of acetoclastic methanogenesis, resulting in nearly stoichiometric accumulation of acetate. CO₂ was produced without lag phase. The δ¹³C of the produced CO₂ was slightly lower in soil grown with cultivated rice versus wild rice, reflecting the δ¹³C of organic matter, which was about −29‰ for cultivated rice soil and about −24‰ for wild rice soil. The δ¹³C of the produced CH₄ and the acetate that accumulated in the presence of CH₃F was much more negative in cultivated versus wild rice soil, mainly since the isotopic fractionation factors for hydrogenotrophic methanogenesis were higher for soil from cultivated rice (α = 1.054) versus wild rice (α = 1.039). However, the percentage contribution of hydrogenotrophic methanogenesis to total CH₄ production was similar in both soils (27-35%). In conclusion, although the two soils exhibited different δ¹³C values of soil organic matter and derived products, they were similar with respect to rates and composition of the methanogenic communities.     

外源腐解微生物的物种组合对土壤微生物群落结构及代谢活性的影响

本文采用饲料类芽孢杆菌(Paenibacillus pabuli,P)、深红紫链霉菌(Streptomyces violaceorubidus,S)和黄绿木霉(Trichoderma aureoviride,T),组合构建了3种单菌剂(P、S和T)、3种两菌种复合菌剂(PT、PS和ST)及1种3菌种复合菌剂(PST),并将之添加到红壤中,监测各菌剂添加后土壤总磷脂脂肪酸(PLFAs)量、特征微生物PLFAs百分含量、土壤呼吸速率及总代谢熵的变化,旨在探明外源腐解微生物的物种组合对土壤微生物群落结构和代谢活性的影响,进而为优化有机物分解菌剂种群配置提供参考。结果显示,添加单菌剂的P、S和T处理及添加两菌种复合菌剂的PT和PS处理,土壤微生物生物量显著增加,增幅17.2%~121.6%(P0.05)。添加外源腐解微生物后,各处理的土壤微生物群落的细菌百分含量基本稳定在79.6%~83.1%,真菌百分含量显著增加8.8%~50.6%;而放线菌百分含量除P和ST处理外,其他处理显著降低9.4%~69.8%。PLFAs数据的主成分分析表明,各外源菌剂处理与CK处理间的群落结构变异由小到大依次为:接种单菌剂的P、S和T处理,接种两菌种复合菌剂的PT、PS和ST处理,接种3菌种复合菌剂的PST处理。添加单菌剂的P、T处理以及添加两菌种复合菌剂的ST处理,在短期内影响了土壤微生物的对数生长,使土壤呼吸速率的峰值分别提高48.7%、53.7%和78.7%;且外源腐解微生物组合的物种数量越多,土壤微生物进入潜伏期所需的时间越长。从外源腐解微生物对土壤肥力的长期影响来看,两菌种复合菌剂ST的添加使土壤微生物代谢活性提高28.9%,因此该处理的土壤碳矿化量增加11.1%;添加单菌剂的S处理使土壤微生物代谢活性显著降低32.4%,因此该处理的土壤碳矿化量仅降低7.3%;而添加两菌种复合菌剂的PS处理和3菌种复合菌剂的PST处理,在保持代谢活性不变的情况下,其土壤碳矿化量也降低5.8%~8.7%,其原因有待进一步研究。综上所述,外源腐解微生物的添加会改变土壤微生物的群落结构及其生长轨迹,且随外源腐解微生物组合的物种数量增多这一干扰程度越大,而土壤微生物代谢活性与外源腐解微生物组合的物种数量无显著相关性。     

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.     

Soil microbial biomass,crop yields,and bacterial community structure as affected by long-term fertilizer treatments under wheat-rice cropping

Soil microbial biomass carbon (SMBC) and nitrogen (SMBN), soil microbial community structure, and crop yields were studied in a long-term (1982–2004) fertilization experiment carried out in Suining, Sichuan province of PR China. Eight treatments included three chemical fertilizer (CF) treatments (N, NP, NPK), three CF + farmyard manure (M) treatments (NM, NPM, NPKM), M alone and no fertilizer (CK) as control. The results showed that the soil microbial biomass was higher in soil treated with CFM than in soil treated with CF alone, and that NPKM gave the highest rice and wheat yields. The SMBC and SMBN were higher after rice than those after wheat cropping. SMBC correlated closely with soil organic matter. Average yields of wheat and rice for 22 years were higher and more stable in the fertilized plots than in control plots. Bacterial community structure was analyzed by PCR-DGGE targeting eubacterial 16S rRNA genes. A higher diversity of the soil bacterial community was found in soil amended with CFM than in other fertilizer treatments. Some specific band emerged in the soil amended with M. The highest diversity of bacterial communities was found in the NPKM treated soil. The bacterial community structures differed in rice and wheat plots. Sequencing of PCR products separated in DGGE showed that some of the common and dominant bands were closely related to Aquicella lusitana and to Acidobacteria. This study demonstrated that mixed application of N, P, and K with additional M amendment increased soil microbial biomass, diversified the bacterial communities and maintained the crop production in the Calcareous Purplish Paddy soil.     

Differential responses of total and active soil microbial communities to long-term experimental N deposition

The relationship between total and metabolically active soil microbial communities can provide insight into how these communities are impacted by environmental change, which may impact the flow of energy and cycling of nutrients in the future. For example, the anthropogenic release of biologically available N has dramatically increased over the last 150 years, which can alter the processes controlling C storage in terrestrial ecosystems. In a northern hardwood forest ecosystem located in Michigan, USA, nearly 20 years of experimentally increased atmospheric N deposition has reduced forest floor decay and increased soil C storage. A microbial mechanism underlies this response, as compositional changes in the soil microbial community have been concomitantly documented with these biogeochemical changes. Here, we co-extracted DNA and RNA from decaying leaf litter to determine if experimental atmospheric N deposition has lowered the diversity and altered the composition of the whole communities of bacteria and fungi (i.e., DNA-based) and well as its active members (i.e., RNA-based). In our experiment, experimental N deposition did not affect the composition, diversity, or richness of the total forest floor fungal community, but did lower the diversity (−8%), as well as altered the composition of the active fungal community. In contrast, neither the total nor active forest floor bacterial community was significantly affected by experimental N deposition. Our results suggest that future rates of atmospheric N deposition can fundamentally alter the organization of the saprotrophic soil fungal community, key mediators of C cycling in terrestrial environments.     

Plant residues do not have an immediate impact on soil bacterial community composition and abundance

Plant residues are often used as soil amendments in laboratory experiments, but they can reportedly release compounds interfering with soil DNA extraction and subsequent molecular biological analyses. Theoretically, for accurate comparison of microbial community composition in soils with and without added plant residues after a period of incubation, no significant difference at the beginning of the experiment is required between the amended and unamended control soils. We mixed plant residue into soil and immediately (within 10 min) commenced DNA extraction, and then performed 16S rRNA gene sequencing and quantitative PCR (qPCR) to determine bacterial community composition and abundance. Soil without plant residue addition served as a control. Five commonly used DNA extraction kits, 16S rRNA gene primer pairs, and soils, and two types (rice straw and alfalfa shoots) and three addition rates (2%, 4%, and 6%; w/w) of plant residue, were tested. In all cases, we found no significant difference in measured bacterial community composition or abundance between the treatments with and without added plant residue.     

Establishment of macro-aggregates and organic matter turnover by microbial communities in long-term incubated artificial soils

The study of interactions between minerals, organic matter (OM) and microorganisms is essential for the understanding of soil functions such as OM turnover. Here, we present an interdisciplinary approach using artificial soils to study the establishment of the microbial community and the formation of macro-aggregates as a function of the mineral composition by using artificial soils. The defined composition of a model system enables to directly relate the development of microbial communities and soil structure to the presence of specific constituents. Five different artificial soil compositions were produced with two types of clay minerals (illite, montmorillonite), metal oxides (ferrihydrite, boehmite) and charcoal incubated with sterile manure and a microbial community derived from a natural soil. We used the artificial soils to analyse the response of these model soil systems to additional sterile manure supply (after 562 days). The artificial soils were subjected to a prolonged incubation period of more than two years (842 days) in order to take temporally dynamic processes into account. In our model systems with varying mineralogy, we expected a changing microbial community composition and an effect on macro-aggregation after OM addition, as the input of fresh substrate will re-activate the artificial soils. The abundance and structure of 16S rRNA gene and internal transcribed spacer (ITS) fragments amplified from total community DNA were studied by quantitative real-time PCR (qPCR) and denaturing gradient gel electrophoresis (DGGE), respectively. The formation of macro-aggregates (>2 mm), the total organic carbon (OC) and nitrogen (N) contents, the OC and N contents in particle size fractions and the CO₂ respiration were determined. The second manure input resulted in higher CO₂ respiration rates, 16S rRNA gene and ITS copy numbers, indicating a stronger response of the microbial community in the matured soil-like system. The type of clay minerals was identified as the most important factor determining the composition of the bacterial communities established. The additional OM and longer incubation time led to a re-formation of macro-aggregates which was significantly higher when montmorillonite was present. Thus, the type of clay mineral was decisive for both microbial community composition as well as macro-aggregation, whereas the addition of other components had a minor effect. Even though different bacterial communities were established depending on the artificial soil composition, the amount and quality of the OM did not show significant differences supporting the concept of functional redundancy.     

Biogeography and biophysicochemical traits link N2O emissions,N2O emission potential and microbial communities across New Zealand pasture soils

The process of denitrification has been studied for decades, with current evidence suggesting that an ecosystem's ability to produce and emit N₂O is controlled both by transient ‘proximal’ regulators (e.g. temperature, moisture, N availability) as well as distal regulators (e.g. soil type, microbial functional diversity, geography). In this study we use New Zealand soils as a model system to test the impact of distal regulators (i.e. geography) on microbial communities and their N₂O emission potential. Using gas chromatography, soil chemical analyses, 16S amplicon sequencing, terminal restriction fragment length polymorphism (T-RFLP) and quantitative PCR (qPCR) on three denitrifier functional genes (nirS, nirK and nosZ), we assessed the factors linked to N₂O emissions across a latitudinal gradient. Results show that soil drainage class, soil texture class, and latitude were powerful regulators of both emissions and emission end products (N₂ vs. N₂O). Mixed models demonstrate that a few variables (including latitude, texture class, drainage class and denitrifier community data [abundance and diversity] amongst others) were enough to predict both the amount and type of gas emitted. In addition we show that microbial community composition (based on 16S rRNA gene sequencing) can also be used to predict both the gas species and quantity emitted.     

Grazing effects on microbial community composition, growth and nutrient cycling in salt marsh and sand dune grasslands

The effect of grazing by large herbivores on the microbial community and the ecosystem functions they provide are relatively unknown in grassland systems. In this study, the impact of grazing upon the size, composition and activity of the soil microbial community was measured in field experiments in two coastal ecosystems: one salt marsh and one sand dune grassland. Bacterial, fungal and total microbial biomass were not systematically affected by grazing across ecosystems, although, within an ecosystem, differences could be detected. Fungal-to-bacterial ratio did not differ with grazing for either habitat. Redundancy analysis showed that soil moisture, bulk density and root biomass significantly explained the composition of phospholipid fatty acid (PLFA) markers, dominated by the distinction between the two grassland habitats, but where the grazing effect could also be resolved. PLFA markers for Gram-positive bacteria were more proportionally abundant in un-grazed, and markers for Gram-negative bacteria in grazed grasslands. Bacterial growth rate (leucine incorporation) was highest in un-grazed salt marsh but did not vary with grazing intensity in the sand dune grassland. We conclude that grazing consistently affects the composition of the soil microbial community in semi-natural grasslands but that its influence is small (7 % of the total variation in PLFA composition), compared with differences between grassland types (89 %). The relatively small effect of grazing translated to small effects on measurements of soil microbial functions, including N and C mineralisation. This study is an early step toward assessing consequences of land-use change for global nutrient cycles driven by the microbial community.