Do earthworms affect dynamics of functional response and genetic structure of microbial community in a lab-scale composting system?

Two laboratory-scale systems were set up (i) composting (without earthworms) and (ii) vermicomposting (with earthworms) and were monitored for 60 days after pre-composting. The physico-chemical parameters (pH, C/N, organic matter, NH(4)(+)-N and ash content) showed similar evolution in both systems except a higher NH(4)(+)-N in the initial vermicomposts. However, principle component analysis (PCA) of enzymatic activities and community level physiological profiles revealed differences in the functional response of microbial communities in compost and vermicompost during maturation. Dehydrogenase activity and bacterial counts indicated a steady decrease in biological activity and population during composting, whereas vermicomposting exhibited higher activity on day 30 and a reduction in bacterial counts on day 10. PCA of denatured gradient gel electrophoresis (DGGE) profiles showed divergent dynamics of bacterial communities in two processes. These results indicated differences in the functional response and genetic structure of microbial community in composts and vermicomposts despite similar changes in their physico-chemical parameters.     

Bioavailability of Cd in a soil–rice system in China: soil type versus genotype effects

Human exposure to toxic heavy metals via dietary intake is of increasing concern. In this regard, the bioavailability of heavy metals in the soil–crop system is considered to be a key factor controlling plant uptake and, therefore, public health risk through food chain transfer [J. Environ. Sci. Health B 34(4) (1999) 681]. In 2002, a pot experiment was conducted to elucidate the relative significance of soil types and rice genotype on the bioavailability, uptake and partitioning of Cd by two rice cultivars with distinct affinity for Cd. The results indicated that the total uptake of Cd and accumulation in grain was dependent on both soil type and genotype effects. Cd spiking enhanced high Cd uptake and partitioning in grain. Inherent differences in soil type effecting Cd bioavailability were less significant under the Cd spiking regime as compared to non-Cd spiking. In the case of Soil-P, with low Cd bioavailability as indicated by the comparatively lower MgCl₂ extractableCd, differences in metal affinity between genotypes dominated uptake. Conversely, inherent differences in soil type affecting Cd bioavailability dominated uptake in the low metal affinity cultivar treatments. Under the experimental conditions evaluated, the positive interaction between soil type and genotype results in elevated levels of Cd in rice grain with the Cd values exceeding the Chinese food guideline limit of 0.2 mg kg^–1. The results indicated that Cd bioavailability and plant uptake is dependent on soil chemical and physical properties affecting Cd mobility, rice genotype and soil pollution status. The results further suggested that caution should be paid to rice production with the new high metal affinity genotypes on soils with inherent Cd bioavailability as with acidic Red Soils of Jiangxi Provinces, China.     

Effect of tillage and straw return on carbon footprints,soil organic carbon fractions and soil microbial community in different textured soils under rice–wheat rotation: a review

Reviews in Environmental Science and Bio/Technology - Measuring the influence of long-term agricultural tillage practices on soil organic carbon (SOC) is of great importance to farmers and...     

Electrokinetic remediation and microbial community shift of β-cyclodextrin-dissolved petroleum hydrocarbon-contaminated soil

Electrokinetic (EK) migration of β-cyclodextrin (β-CD), which is inclusive of total petroleum hydrocarbon (TPH), is an economically beneficial and environmentally friendly remediation process for oil-contaminated soils. Remediation studies of oil-contaminated soils generally prepared samples using particular TPHs. This study investigates the removal of TPHs from, and electromigration of microbial cells in field samples via EK remediation. Both TPH content and soil respiration declined after the EK remediation process. The strains in the original soil sample included Bacillus sp., Sporosarcina sp., Beta proteobacterium, Streptomyces sp., Pontibacter sp., Azorhizobium sp., Taxeobacter sp., and Williamsia sp. Electromigration of microbial cells reduced the biodiversity of the microbial community in soil following EK remediation. At 200 V m⁻¹ for 10 days, 36% TPH was removed, with a small population of microbial cells flushed out, demonstrating that EK remediation is effective for the present oil-contaminated soils collected in field.     

Inputs of seabird guano alter microbial growth,community composition and the phytoplankton–bacterial interactions in a coastal system

Seabird guano enters coastal waters providing bioavailable substrates for microbial plankton, but their role in marine ecosystem functioning remains poorly understood. Two concentrations of the water soluble fraction (WSF) of gull guano were added to different natural microbial communities collected in surface waters from the Ría de Vigo (NW Spain) in spring, summer, and winter. Samples were incubated with or without antibiotics (to block bacterial activity) to test whether gull guano stimulated phytoplankton and bacterial growth, caused changes in taxonomic composition, and altered phytoplankton–bacteria interactions. Alteromonadales, Sphingobacteriales, Verrucomicrobia and diatoms were generally stimulated by guano. Chlorophyll a (Chl a) concentration and bacterial abundance significantly increased after additions independently of the initial ambient nutrient concentrations. Our study demonstrates, for the first time, that the addition of guano altered the phytoplankton–bacteria interaction index from neutral (i.e. phytoplankton growth was not affected by bacterial activity) to positive (i.e. phytoplankton growth was stimulated by bacterial activity) in the low-nutrient environment occurring in spring. In contrast, when environmental nutrient concentrations were high, the interaction index changed from positive to neutral after guano additions, suggesting the presence of some secondary metabolite in the guano that is needed for phytoplankton growth, which would otherwise be supplied by bacteria.     

Fertilization effects on microbial community composition and aggregate formation in saline‐alkaline soil

Plant and Soil - Soil was sampled (0–20 cm) from a 5-year Yellow River Delta paddy field experiment: no fertilizers (Control), mineral fertilizers (NPK), and NPK plus organic...     

Linking microbial community structure to β-glucosidic function in soil aggregates

To link microbial community 16S structure to a measured function in a natural soil, we have scaled both DNA and β-glucosidase assays down to a volume of soil that may approach a unique microbial community. β-Glucosidase activity was assayed in 450 individual aggregates, which were then sorted into classes of high or low activities, from which groups of 10 or 11 aggregates were identified and grouped for DNA extraction and pyrosequencing. Tandem assays of ATP were conducted for each aggregate in order to normalize these small groups of aggregates for biomass size. In spite of there being no significant differences in the richness or diversity of the microbial communities associated with high β-glucosidase activities compared with the communities associated with low β-glucosidase communities, several analyses of variance clearly show that the communities of these two groups differ. The separation of these groups is partially driven by the differential abundances of members of the Chitinophagaceae family. It may be observed that functional differences in otherwise similar soil aggregates can be largely attributed to differences in resource availability, rather than to the presence or absence of particular taxonomic groups.     

Explaining the variation in the soil microbial community: do vegetation composition and soil chemistry explain the same or different parts of the microbial variation?

Aim

To assess whether vegetation composition and soil chemistry explain the same or different parts of the variation in the soil microbial community (SMC).

Method

The above and below-ground communities and soil chemical properties were studied along a successional gradient from moorland to deciduous woodland. The SMC was assessed using PLFAs and M-TRFLPs. Using variance partitioning, Co-Correspondence Analysis (CoCA) and Canonical Correspondence Analysis (CCA), the variation (total inertia) in the SMC was partitioned into variation which was uniquely explained by either plant composition or soil chemistry, variation explained by both soil chemistry and plant composition, and unexplained variation.

Results

Plant community composition uniquely explained 30, 13, 16 and 20% of the inertia and soil chemistry uniquely explained 5, 18, 9 and 9% of the inertia in the archaeal TRFLPs, bacterial TRFLPs, fungal TRFLPs and all PLFAs, respectively.

Conclusion

For the first time, variance partitioning was used to include data from a CoCA; although the current limits of such an approach are shown, this study illustrates the potential of such analyses and shows that soil chemistry and plant composition are, in substantial amounts, explaining different parts of the variation within the SMC. This marks an important step in furthering our understanding of the relative importance of different drivers of change in the SMC.     

Accumulation of rice prolamin–GFP fusion proteins induces ER-derived protein bodies in transgenic rice calli

Key message

We showed that rice prolamin polypeptides formed ER-derived PBs in transgenic rice calli, and that this heterologous transgene expression system is suitable for studying the mechanism of rice PB-I formation.

Abstract

Rice prolamins, alcohol-soluble seed storage proteins, accumulate directly within the rough endoplasmic reticulum (ER) lumen, leading to the formation of ER-derived type I protein bodies (PB-Is) in rice seed. Because rice prolamins do not possess a well-known ER retention signal such as K(H)DEL, or a unique sequence for retention in the ER such as a tandem repeat domain of maize and wheat prolamins, the mechanisms of prolamin accumulation in the ER and PB-I formation are poorly understood. In this study, we examined the formation mechanisms of PBs by expressing four types of rice prolamin species fused to green fluorescent protein (GFP) in transgenic rice calli. Each prolamin–GFP fusion protein was stably accumulated in rice calli and formed ER-derived PBs. In contrast, GFP fused with the signal peptide of prolamin was secreted into the intercellular space in rice calli. In addition, each of the four types of prolamin–GFP fusion proteins was co-localized with the ER chaperone binding protein. These results suggest that the mature polypeptide of prolamin is capable of being retained in the ER and induce the formation of PBs in non-seed tissue, and that the rice callus heterologous transgene expression system is useful for studying the mechanisms of rice PB-I formation.     

Stoichiometric homeostasis in response to variable water and nutrient supply in a Robinia pseudoacacia plant–soil system

刺槐植物-土壤系统生态化学计量内稳性对水分和养分变异的响应特征 所有生物体都需要一定比例的元素来维持正常的生理代谢过程,它们的可塑性取决于它们利用外部资源的效率。阐明不同资源供应水平下植物、土壤和土壤微生物生物量生态化学计量特征之间的相互作用非常重要。本研究以一年生刺槐(Robinia pseudoacacia)幼苗为研究对象,测定不同水平水分、氮素和磷素处理下刺槐叶片、细根、土壤和微生物生物量C、N、P含量及其化学计量学指标。结果表明,刺槐叶片、细根、土壤和微生物生物量C、N、P含量及其化学计量特征会对其生存环境水分和养分条件的变化表现出一定程度的可塑性;方差分解分析结果表明,细根计量比解释了微生物生物量计量比方差的很大一部分;结构方程模型进一步揭示了细根计量比和叶片计量比是影响土壤微生物生物量C:N和C:P 的两个直接因素,而细根计量比具有较大的直接作用。此外,内稳性特征分析表明土壤微生物生物量C 和C:P对土壤养分变化较为敏感,其他指标均具有内稳性。这些结果明确了土壤微生物生物量化学计量的重要性,提高我们对不同生境水分和养分供应水平下植物-土壤系统养分循环机理的认识。     

Changes in soil phosphorus fractions in response to long‐term phosphate fertilization under sole cropping and intercropping of maize and faba bean on a calcareous soil

Plant and Soil - Understanding how soil phosphorus (P) fractions change is critical to achieve more efficient soil P use in a highly P-sorbing calcareous soil. The fields were managed without or...     

Is vegetation composition or soil chemistry the best predictor of the soil microbial community?

With the species composition and/or functioning of many ecosystems currently changing due to anthropogenic drivers it is important to understand and, ideally, predict how changes in one part of the ecosystem will affect another. Here we assess if vegetation composition or soil chemistry best predicts the soil microbial community. The above and below-ground communities and soil chemical properties along a successional gradient from dwarf shrubland (moorland) to deciduous woodland (Betula dominated) were studied. The vegetation and soil chemistry were recorded and the soil microbial community (SMC) assessed using Phospholipid Fatty Acid Extraction (PLFA) and Multiplex Terminal Restriction Fragment Length Polymorphism (M-TRFLP). Vegetation composition and soil chemistry were used to predict the SMC using Co-Correspondence analysis and Canonical Correspondence Analysis and the predictive power of the two analyses compared. The vegetation composition predicted the soil microbial community at least as well as the soil chemical data. Removing rare plant species from the data set did not improve the predictive power of the vegetation data. The predictive power of the soil chemistry improved when only selected soil variables were used, but which soil variables gave the best prediction varied between the different soil microbial communities being studied (PLFA or bacterial/fungal/archaeal TRFLP). Vegetation composition may represent a more stable ‘summary’ of the effects of multiple drivers over time and may thus be a better predictor of the soil microbial community than one-off measurements of soil properties.     

Gain of deleterious function causes an autoimmune response and Bateson–Dobzhansky–Muller incompatibility in rice

Reproductive isolation plays an important role in speciation as it restricts gene flow and accelerates genetic divergence between formerly interbreeding population. In rice, hybrid breakdown is a common reproductive isolation observed in both intra and inter-specific crosses. It is a type of post-zygotic reproductive isolation in which sterility and weakness are manifested in the F₂ and later generations. In this study, the physiological and molecular basis of hybrid breakdown caused by two recessive genes, hbd2 and hbd3, in a cross between japonica variety, Koshihikari, and indica variety, Habataki, were investigated. Fine mapping of hbd2 resulted in the identification of the causal gene as casein kinase I (CKI1). Further analysis revealed that hbd2-CKI1 allele gains its deleterious function that causes the weakness phenotype by a change of one amino acid. As for the other gene, hbd3 was mapped to the NBS-LRR gene cluster region. It is the most common class of R-gene that triggers the immune signal in response to pathogen attack. Expression analysis of pathogen response marker genes suggested that weakness phenotype in this hybrid breakdown can be attributed to an autoimmune response. So far, this is the first evidence linking autoimmune response to post-zygotic isolation in rice. This finding provides a new insight in understanding the molecular and evolutionary mechanisms establishing post-zygotic isolation in plants.     

Long-term manuring and fertilization effects on soil organic carbon pools under a wheat–maize cropping system in North China Plain

The effects of organic manure and chemical fertilizer on total soil organic carbon (C _T), water-soluble organic C (C _WS), microbial biomass C (C _MB), labile C (C _L), C mineralization, C storage and sequestration, and the role of carbon management index (CMI) in soil quality evaluation were studied under a wheat–maize cropping system in a long-term experiment, which was established in 1989 in the North China Plain. The experiment included seven treatments: (1) OM: application of organic manure; (2) 1/2OMN: application of half organic manure plus chemical fertilizer NPK; (3) NPK: balanced application of chemical fertilizer NPK; (4) NP: application of chemical fertilizer NP; (5) PK: application of chemical fertilizer PK; (6) NK: application of chemical fertilizer NK; and (7) CK: unfertilized control. Application of organic manure (OM and 1/2OMN) was more effective for increasing C _T, C _WS, C _MB, C _L, C mineralization, and CMI, as compared with application of chemical fertilizer alone. For the chemical fertilizer treatments, balanced application of NPK (treatment 3) showed higher C _T, C _WS, C _MB, C _L, C mineralization, and CMI than the unbalanced use of fertilizers (treatments 4, 5, and 6). The C storage in the OM and 1/2OMN treatments were increased by 58.0% and 26.6%, respectively, over the NPK treatment, which had 5.9–25.4% more C storage than unbalanced use of fertilizers. The contents of C _WS, C _MB, and C _L in organic manure treatments (treatments 1 and 2) were increased by 139.7–260.5%, 136.7–225.7%, and 150.0–240.5%, respectively, as compared to the CK treatment. The CMI was found to be a useful index to assess the changes of soil quality induced by soil management practices due to its significant correlation with soil bulk density and C fractions. The OM and 1/2OMN treatments were not a feasible option for farmers, but a feasible option for sequestering soil carbon, especially for the OM treatment. The NPK treatment was important for increasing crop yields, organic material inputs, and soil C fractions, so it could increase the sustainability of cropping system in the North China Plain.     

Influence of co-inoculation of bacteria-cyanobacteria on crop yield and C–N sequestration in soil under rice crop

The performance of three selected bacterial strains—PR3, PR7 and PR10 (Providencia sp., Brevundimonas sp., Ochrobacterium sp.) and three cyanobacterial strains CR1, CR2 and CR3 (Anabaena sp., Calothrix sp., Anabaena sp.), and their combinations was evaluated in a pot experiment with rice variety Pusa-1460, comprising 51 treatments along with recommended fertilizer controls. Highest yield enhancement of 19.02% was recorded in T12 (CR2), over control, while significant enhancement in nitrogen fixing potential was recorded in treatments involving combination of bacterial-cyanobacterial strains—T37 (PR3 + CR1 + CR3) and T21 (PR7 + CR1). Organic carbon was significantly increased in all microbe-inoculated treatments, which could be correlated with microbial biomass carbon values and activities of all the enzymes tested in our study. Also, panicle weight and plant biomass were highly correlated with soil microbial carbon. Comparative evaluation revealed the superior performance of strains CR2, CR1 (both Anabaena sp.) and PR10 (Ochrobacterium sp.) in increasing the growth and grain yield of rice and improving soil health, besides N (nitrogen) savings of 40–80 kg ha⁻¹. The study for the first time illustrated the positive effects of co-inoculation of bacterial and cyanobacterial strains for integrated nutrient management of rice crop.     

Do temperate tree species diversity and identity influence soil microbial community function and composition?

Studies of biodiversity–ecosystem function in treed ecosystems have generally focused on aboveground functions. This study investigates intertrophic links between tree diversity and soil microbial community function and composition. We examined how microbial communities in surface mineral soil responded to experimental gradients of tree species richness (SR ), functional diversity (FD ), community‐weighted mean trait value (CWM ), and tree identity. The site was a 4‐year‐old common garden experiment near Montreal, Canada, consisting of deciduous and evergreen tree species mixtures. Microbial community composition, community‐level physiological profiles, and respiration were evaluated using phospholipid fatty acid (PLFA ) analysis and the MicroResp^? system, respectively. The relationship between tree species richness and glucose‐induced respiration (GIR ), basal respiration (BR ), metabolic quotient (qCO ₂) followed a positive but saturating shape. Microbial communities associated with species mixtures were more active (basal respiration [BR ]), with higher biomass (glucose‐induced respiration [GIR ]), and used a greater number of carbon sources than monocultures. Communities associated with deciduous tree species used a greater number of carbon sources than those associated with evergreen species, suggesting a greater soil carbon storage capacity. There were no differences in microbial composition (PLFA ) between monocultures and SR mixtures. The FD and the CWM of several functional traits affected both BR and GIR . In general, the CWM of traits had stronger effects than did FD , suggesting that certain traits of dominant species have more effect on ecosystem processes than does FD . Both the functions of GIR and BR were positively related to aboveground tree community productivity. Both tree diversity (SR ) and identity (species and functional identity—leaf habit) affected soil microbial community respiration, biomass, and composition. For the first time, we identified functional traits related to life‐history strategy, as well as root traits that influence another trophic level, soil microbial community function, via effects on BR and GIR .     

The difference of potassium dynamics between yellowish red soil and yellow cinnamon soil under rapeseed (Brassica napus L.)–rice (Oryza sativa L.) rotation

To increase the use efficiency of potassium (K) fertilizer, special attention was paid to the dynamics of soil K in the root zone and non-root zone. Difference in K dynamics between yellowish red soil and yellow cinnamon soil under rapeseed (Brassica napus L.)rice (Oryza sativa L.) rotation was studied using a rhizobox system. Results showed that soil water soluble K (Sol-K) and exchangeable K (Ex-K) in the root zone of both soils were reduced in the early stage of rapeseed growth. Along with plant growth and K uptake, soil Sol-K in the inner (0–20 mm to root zone), middle (20–40 mm) and outer (40–60 mm) compartments of the non-root zone of yellowish red soil migrated towards the root zone. As a result, soil Ex-K was transformed into Sol-K. The changes in soil Sol-K and Ex-K in the non-root zone of yellow cinnamon soil were similar to yellowish red soil, and soil non-exchangeable K (Nonex-K) in the root zone also decreased significantly. In the early stage of rice growth, waterlogging promoted diffusion of soil Sol-K from non-root zone to root zone and transformation of Ex-K into Sol-K. Along with the growth of rice and K uptake, soil Ex-K in each compartment of yellowish red soil decreased significantly. Soil Sol-K and Ex-K in the yellow cinnamon soil declined to a certain extent, and then remained unchanged, while soil Nonex-K kept on decreasing. It revealed that the plants first absorbed K in the root zone, of which K reserve was replenished by a gradual diffusion of K from the non-root zone. The closer to the root zone, the greater the contribution to K uptake by plants. Within one rotation cycle, Ex-K and Sol-K in yellowish red soil were the main forms of K available to the plants, and little Nonex-K could be absorbed. However, in the yellow cinnamon soil, Nonex-K was the main form of K available to the plants, followed by Ex-K and Sol-K.