Microbial community responsible for the decomposition of rice straw in a paddy field: estimation by phospholipid fatty acid analysis

To estimate the microbial communities responsible for rice straw decomposition in paddy field, phospholipid fatty acid (PLFA) composition of leaf sheaths and blades was analyzed during the decomposition of both residues under upland conditions after harvest and under flooded conditions at the time of transplanting of rice plants. In addition, rice straw that had been placed in the field under upland conditions (November to April) was taken out in spring, and placed again in the same field under flooded conditions at the time of transplanting. High proportions of the branched-chain PLFAs were observed under flooded conditions (June to September); the proportions of straight mono-unsaturated and straight poly-unsaturated PLFAs were high under upland conditions in the winter season for 4 months. The dominant PLFAs in straight mono-unsaturated, straight poly-unsaturated and branched-chain PLFA groups were 18:19, 18:17 and 16:17c, 18:26c and i15:0, i17:0 and ai15:0, respectively, under both upland and flooded conditions. These findings indicated the important roles of Gram-negative bacteria and fungi under upland conditions and of Gram-positive bacteria and anaerobic Gram-negative bacteria under flooded conditions. Cluster analysis of PLFA composition showed the difference of community structure of microbiota in rice straw between upland and flooded conditions. In addition principal component analysis revealed the difference between leaf sheaths and blades under upland conditions and indicated that the content of straight unsaturated PLFAs (sheaths > blades) characterized their community structures.     

Biodegradation of Cry1Ab protein from Bt transgenic rice in aerobic and flooded paddy soils

Degradation of Cry1Ab protein from Bt transgenic rice was examined under both aerobic and flooded conditions in five paddy soils and in aqueous solutions. The hydrolysis rate of Cry1Ab protein in aqueous solutions was correlated inversely with the solution pH in the range of 4.0 to 8.0, and positively with the initial concentration of Cry1Ab protein. Rapid degradation of Cry1Ab protein occurred in paddy soils under aerobic conditions, with half-lives ranging from 19.6 to 41.3 d. The degradation was mostly biotic and not related to any specific soil property. Degradation of the Cry1Ab protein was significantly prolonged under flooded conditions compared with aerobic conditions, with half-lives extended to 45.9 to 141 d. These results suggest that the toxin protein, when introduced into a paddy field upon harvest, will probably undergo rapid removal after the field is drained and exposed to aerobic conditions.     

The microbial community composition changes rapidly in the early stages of decomposition of wheat residue

It is generally accepted that during the early stages of residue decomposition, easily available compounds are decomposed, leading to a relative increase in more recalcitrant compounds in the later stages of decomposition and that these changes in substrate availability are associated with changes in microbial community composition. However most studies on residue decomposition are conducted over several weeks or months; little is known about the changes in microbial community composition in the first weeks of decomposition. To address this knowledge gap, we incubated wheat residues inoculated with a microbial suspension in mesh bags buried in sand for 30 days, with sampling on days 0, 2, 4, 6, 8, 10, 15, 20, 25 and 30. Of the C added with the residues, 10, 18 and 25% had been respired on days 10, 20 and 30, respectively. The sum of PLFAs (phospholipid fatty acids), as an indicator of microbial biomass, increased strongly in the first 4 days and then decreased. The concentration of bacterial fatty acids was maximal on days 2 and 4, whereas the concentration of fungal fatty acids peaked on day 15. Microbial community composition (based on PLFA patterns) changed rapidly, with significant changes in the first 8 days and from day 8 to day 20. There were no significant changes in microbial community composition after day 20. The concentration of water-soluble C decreased strongly in the first 8 days, suggesting that the rapid changes in microbial community in this period are related to the changes in water-soluble C. Residue C chemistry, assessed by ¹³C NMR spectroscopy, changed little during the incubation period. This study showed that microbial community composition in decomposing residues changes rapidly in the first 1-2 weeks, which is, at least partly, the result of competition for the easily available compounds in the water-soluble fraction. After depletion of the water-soluble compounds, the microbial community composition changes more slowly.     

Microbial communities responsible for the decomposition of rice straw compost in a Japanese rice paddy field determined by phospholipid fatty acid (PLFA) analysis

To identify the microbial communities responsible for the decomposition of rice straw compost in soil during the rice cultivation period, phospholipid fatty acid (PLFA) composition of rice straw compost was determined by periodically sampling the compost from a Japanese rice field under flooded conditions. About 21% of the compost was decomposed within a period of 3 months. The total amount of PLFAs, as an indicator of microbial biomass, was significantly lower under drained conditions than under flooded conditions and was relatively constant during the flooding period. This indicates that the microbial biomass in the compost samples did not increase during the gradual decomposition of rice straw compost under flooded conditions. The proportion of branched-chain PLFAs (biomarker of Grampositive and anaerobic Gram-negative bacteria) slightly decreased during the early period after placement, and increased gradually afterwards. Among the branched-chain PLFAs, i15:0, ail5:0, i16:0 and i17:0 PLFAs predominated and their proportions increased gradually except for i16:0. The proportion of straight mono-unsaturated PLFAs (biomarker of Gramnegative bacteria) was almost constant throughout the period, and 18:1ω9 and 18:1ω7 PLFAs predominated. The proportion of straight poly-unsaturated PLFAs as a biomarker of eukaryotes including fungi was also constant throughout the period, except for a decrease under drained conditions. Straight poly-unsaturated PLFAs consisted mainly of 18:2ω6c PLFA. Therefore, these results suggest that the proportions of Gram-positive and anaerobic Gram-negative bacteria increased during the decomposition of rice straw compost in flooded paddy field. Statistical analyses enabled to divide PLFA patterns of microbiota in the rice straw compost into two groups, one group consisting of rice straw compost samples collected before mid-season drainage and the other of samples collected after mid-season drainage. Small squared distances among samples in cluster analysis indicated that the community structure of microbiota was similar to each other as a whole. These results suggest that the microbial communities changed gradually during the period of placement, and that mid-season drainage may have affected the community structure of microbiota. Principal component analysis of the PLFA composition suggested that the succession of microbiota along with the decomposition in flooded soil was similar between rice straw compost and rice straw and that the changes in the community structure during the decomposition in flooded soil were more conspicuous for rice straw than for rice straw compost.     

Molecular phylogenetic analysis of a soil microbial community in a soybean field

We report here the phylogenetic characterization of small subunit rRNA gene sequences obtained by polymerase chain reaction (PCR) amplification of mixed population DNA extracted directly from soil in a soybean field without culturing the organisms. The phylogenetic analysis of 17 soil clones by the neighbour-joining method shows that the soil sample contained broadly diverse prokaryotes; a clone related to archaea, a clone to gram-positive bacteria with high G+C contents, two clones to green sulphur bacteria, four clones to proteobacteria, and nine clones were not in clusters of any previously reported bacterial groups, which suggests they belong to members of novel groups in Bacteria. In addition, the archaeal sequence, FIE16, is phylogenetically similar to ANTARCTIC 12, a clone obtained from surface waters of Antarctica by PCR. Their occurrence in both the ocean and soil suggests a global distribution of this archaeal group. In conclusion, rRNA gene sequences recovered from soil biomass document the occurrence of many more bacterial lingeages than have been recognized previously through cultivation-based techniques.     

Faster residue decomposition of brittle stem rice mutant due to finer breakage during threshing

In intensive tropical rice (Oryza sativa L.) cropping systems with short fallows, it would be advantageous that rice straw decompose fast enough to facilitate land preparation and planting of the subsequent crop. The straw of a brittle stem rice mutant of IR68 was tested for more rapid decomposition compared with non-brittle IR68 straw. The hypothesis was that the brittle mutant straw would break into smaller pieces during threshing, and that both the smaller piece size and the differences in biochemical straw composition would enable more rapid decomposition. Brittle straw broke into smaller pieces than non-brittle straw during a replicated trial of three threshing methods: hand threshing, pedal threshing, and axial-flow machine threshing. In a litter bag study to determine the effect of straw piece size on decomposition rate of each straw type over 10 weeks, smaller straw pieces decomposed faster than larger pieces as indicated by changes in amount of straw and its C/N ratio over time (P < 0.05), but there was no significant difference between straw types at the same size. It was concluded that the finer breakage of brittle straw during field operations is likely to be more important than the biochemical differences in overall residue decomposition rate.     

Litterbag decomposition of residues from Bacillus thuringiensis (Bt) rice hybrids and the parental lines under multiple field conditions

Purpose

The cultivation of genetically modified (GM) crops has raised environmental concerns, since large amounts of plant materials remain in the field after harvesting. Specific proteins of GM crops might negatively impact soil ecosystem by changing residue decomposition dynamics. Particularly, the residue decomposition of crop-wild hybrids, which were formed through transgene escape to wild population, remains unexplored.

Materials and methods

We used litter bags to assess residue (leaves, stems and roots) decomposition dynamics of two stacked genes from Bacillus thuringiensis (Bt) Cry1Ac and the sck (a modified CpTI gene encoding a cowpea trypsin-inhibitor) (Bt/CpTI) rice lines (Kefeng-6 and Kefeng-8), a non-transgenic rice near isoline (Minghui86), wild rice (Oryza rufipogon) and Bt wild rice at three sites. The enzyme-linked immunosorbent assay (ELISA) was used to monitor the changes of the Cry1Ac protein in Bt rice residues.

Results and discussion

Mass remaining, total N and total C concentrations of rice residues declined over time and varied among plant tissues, with significant differences among cultivar, crop-wild hybrids and wild rice, but no differences between Bt and non-Bt rice cultivars. The initial concentration of Cry1Ac was higher in leaves and stems than in roots and was different between rice types. The degradation dynamics of Cry1Ac fitted best to a first-order kinetics model and correlated with the level of total nitrogen in residues but did not correlate with the mass decomposition rate. The predicted DT50 (50 % degradation time) of the protein ranged from 10.7 to 63.6 days, depending on plant types, parts and burial sites. By the end of the study (~170 days), the protein was present in low concentration in the remaining residues.

Conclusions

Our results suggest that the impacts of the stacked Bt/CpTI gene inserts on the decomposition dynamics of rice residues are insignificant.     

Modeling within field variation of the compaction layer in a paddy rice field using a proximal soil sensing system

A key characteristic of flooded paddy fields is the plough pan. This is a sub‐soil layer of greater compaction and bulk density, which restricts water losses through percolation. However, the thickness of this compacted layer can be inconsistent, with consequences such as variable percolation and leaching losses of nutrients, which therefore requires precision management of soil water. Our objective was to evaluate a methodology to model the thickness of the compacted soil layer using a non‐invasive electromagnetic induction sensor (EM38‐MK2). A 2.7 ha alluvial non‐saline paddy rice field was measured with a proximal soil sensing system using the EM38‐MK2 and the apparent electrical conductivity (EC_a) of the wet paddy soil was recorded at a high‐resolution (1.0 × 0.5 m). Soil bulk density (n = 10) was measured using undisturbed soil cores, which covered locations with large and small EC_a values. At the same locations (within 1 m²) the depth of the different soil layers was determined by penetrometer. Then a fitting procedure was used to model the EC_a – depth response functions of the EM38‐MK2, which involved solving a system of non‐linear equations and a R² value of 0.89 was found. These predictions were evaluated using independent observations (n = 18) where a Pearson correlation coefficient of 0.87 with an RMSEE value of 0.03 m was found. The EC_a measurements allowed the detail estimation of the compacted layer thickness. The link between water percolation losses and thickness of the compacted layer was confirmed by independent observations with an inverse relationship having a Pearson correlation coefficient of 0.89. This rapid, non‐invasive and cost‐effective technique offers new opportunities to measure differences in the thickness of compacted layers in water‐saturated soils. This has potential for site‐specific soil management in paddy rice fields.     

Faster anaerobic decomposition of a brittle straw rice mutant: Implications for residue management

Rice (Oryza sativa) in Asia is typically grown on submerged soils in intensive cropping systems with only a brief interval between harvest of one crop and planting of the next. Incorporation of crop residues can be challenging because the fallow period between crops is often too short to allow sufficient decomposition. During early stages of anaerobic residue decomposition in flooded soils, plant growth may be inhibited by nutrient immobilization or by the production of potentially toxic organic acids. Straw from a brittle stem mutant of rice (Oryza sativa L. var. IR68) was tested in a 30-d incubation experiment under continuously flooded conditions in a greenhouse to determine if it would decompose more rapidly than the non-brittle phenotype, thereby allowing shorter fallow time between crops. Brittle straw decomposed faster, as indicated by 51% total C loss as CO₂ or CH₄ within 3 weeks of incorporation, compared with 28% for non-brittle straw. However, brittle straw also produced a significantly higher (P<0.0001) amount of formic, acetic, aconitic, propionic, and butyric acids than non-brittle straw. There was no difference in soil N immobilization pattern between the two straw types, or in P or K availability in the soil, perhaps due to the short duration of the experiment. To maximize the potential advantage of faster decomposition of brittle straw in intensive rice cropping systems, it may be helpful to manage water for sufficient soil aeration to mitigate the negative organic acid and methane production effects.     

Bacterial community in plant residues in a Japanese paddy field estimated by RFLP and DGGE analyses

Plant residues (PRs) are “hot spots” of microbial activities in soil. PRs with the size more than 0.5 mm were collected from a Japanese paddy field during rice cultivation period (from May to September) and fractionated into four categories by size (>4, 2-4, 1-2, and 0.5-1 mm) using sieves. Restriction fragment length polymorphism (RFLP) and denaturing gradient gel electrophoresis (DGGE) patterns were compared among the fractions after DNA extraction from the PRs and PCR amplification. The total amount of PRs with the size over 0.5 mm decreased in the field with the first-order kinetics (r²=0.810, p<0.01) with time from rice transplanting to harvest. RFLP analysis showed that the bacterial community structure in PRs with the 0.5-2 mm fraction was different from that in PRs with the >2 mm fraction and the latter community structure changed after the midseason drainage. In contrast, the DGGE patterns of the bacterial community in the PRs indicated the succession from June to September during rice cultivation forming three major groups irrespective of the fraction size. Sequence analysis of DGGE bands showed that Firmicutes (clostridia), α-, γ-, δ-Proteobacteria (myxobacteria), Nitrospira, Acidobacteria, Bacteroidetes, Verrucomicrobia and Spirochaetes were predominant members in the PRs irrespective of fraction size.     

Carbon flux from decomposing 13C-labeled transgenic and nontransgenic parental rice straw in paddy soil

Purpose

Genetic modification of Bt rice may affect straw decomposition and soil carbon pool under flood conditions. This study aims to assess the effects of cry gene transformation in rice on the residue decomposition and fate of C from residues under flooded conditions.

Materials and methods

A decomposition experiment was set up using ¹³C-enriched rice straws from transgenic and nontransgenic Bt rice to evaluate the soil C dynamics and CH₄ or CO₂ emission rates in the root and non-root zones. The concentrations and stable carbon isotope compositions of the soil organic carbon (SOC), dissolved organic carbon (DOC), microbial biomass carbon (MBC), CH₄, and CO₂ of the root and non-root zones were determined from 7 to 110 days after rice straw incorporation.

Results and discussion

Rice straw incorporation into soil significantly increased the SOC, DOC, and MBC concentrations and the CH₄ and CO₂ emission rates. The percentage of ¹³C-SOC remaining in the root zone was significantly lower than that in the non-root zone with rice straw decomposition. The DOC and MBC concentrations significantly increased in both the root and non-root zones between 0 and 80 days after rice straw incorporation. However, no significant differences were found after Bts (Bt rice straw added into soil) and Cks (nontransgenic Bt rice straw added into soil) incorporation in the root and non-root zones. This result may be attributed to the priming effects of sufficient oxygen and nutrients on straw degradation in the root zone.

Conclusions

Bt gene insertion did not affect the SOC, DOC, and MBC concentrations and the CH₄ and CO₂ emission rates in both the root and non-root zones. However, rice straw incorporation and root exudation significantly increased the SOC, DOC, and MBC concentrations and the CH₄ and CO₂ emission rates.     

Soil C balance in a long-term field experiment in relation to the size of the microbial biomass

Soil C balances were calculated in a field experiment started in 1956. Treatments include a fallow and soils receiving different N fertilizers or organic amendments. By assuming the absence of a priming effect, the degree of mineralization of crop residues and organic amendments was calculated. Crop residue mineralization was not affected by a more than 50% decrease in the size of the microbial biomass in soil fertilized with (NH₄)₂SO₄, which had caused the pH of this soil to drop from 6.6 to 4.4. More C had accumulated per unit C input in peat-and sewage sludge-amended soils than in any of the other soils, suggesting that peat and sewage sludge were more resistant to microbial attack. Recalcitrance of substrate C was an adequate explanation for the low ratio of biomass C to soil C in the peat-amended soils, but not in the sewage sludge-amended soil. There was a close linear relationship (r=0.94) between the content of microbial biomass C in the soil measured in 1990 and cumulative C losses from the soil since 1956. Compared to the relationship between soil biomass C and soil organic C concentrations, the linear relationship between microbial C and cumulative C losses suggested that the significantly reduced biomass in the sewage sludge-amended soil was at least partially due to the presence of toxic substances (presumably elevated heavy metal concentrations) in this soil and was probably not affected by the somewhat low pH (5.3) in this soil.     

Soil microbial dynamics in maize-growing soil under different tillage and residue management systems

The long-term impact of tillage and residue management on soil microorganisms was studied over the growing season in a sandy loam to loamy sand soil of southwestern Quebec, growing maize (Zea mays L.) monoculture. Tillage and residue treatments were first imposed on plots in fall 1991. Treatments consisted of no till, reduced tillage, and conventional tillage with crop residues either removed from (−R) or retained on (+R) experimental plots, laid out in a randomized complete block design. Soil microbial biomass carbon (SMB-C), soil microbial biomass nitrogen (SMB-N) and phospholipid fatty acid (PLFA) contents were measured four times, at two depths (0-10 and 10-20 cm), over the 2001 growing season. Sample times were: May 7 (preplanting), June 25, July 16, and September 29 (prior to corn harvest). The effect of time was of a greater magnitude than those attributed to tillage or residue treatments. While SMB-C showed little seasonal change (160 μg C g⁻¹ soil), SMB-N was responsive to post-emergence mineral nitrogen fertilization, and PLFA analysis showed an increase in fungi and total PLFA throughout the season. PLFA profiles showed better distinction between sampling time and depth, than between treatments. The effect of residue was more pronounced than that of tillage, with increased SMB-C and SMB-N (61 and 96%) in +R plots compared to −R plots. This study illustrated that measuring soil quality based on soil microbial components must take into account seasonal changes in soil physical and chemical conditions.     

Neither transgenic Bt maize (MON863) nor tefluthrin insecticide adversely affect soil microbial activity or biomass: A 3-year field analysis

Laboratory and greenhouse studies on transgenic Bacillus thuringiensis (Bt) maize have drawn attention to the persistence and activity of the Cry proteins in soil and their potential effects on soil microorganisms, but there have been few field assessments that evaluate the effects of Bt maize with those of insecticides on soil microbial populations. This study was conducted to determine the effects of Cry3Bb Bt maize with those of the insecticide tefluthrin on soil microbial biomass and activity in the field over a 3-year cropping cycle. The recently commercialized maize variety YieldGard^® Rootworm (MON863), which produces the Cry3Bb protein, was grown along with a non-Bt isoline with and without tefluthrin applied at planting. Microbial biomass, nitrogen (N) mineralization potential, short-term nitrification rate, and respiration rate were measured in rhizosphere and bulk soil samples collected from three replicate field plots just before planting, at anthesis, and at harvest in each year. There were clear seasonal effects on microbial biomass and activity in the field soils—as represented by the consistent changes in all measured variables across years and sampling times. Differences in the measured variables were also sometimes observed between bulk and rhizosphere soil. However, there were no adverse effects of either the Bt or non-Bt maize with insecticide applied compared to the non-Bt controls; on the contrary, microbial biomass and soil respiration data suggested a stimulatory effect of the Bt genotype, particularly in comparison to the non-Bt isoline. Although ‘higher’ does not necessarily mean ‘better’, the higher microbial biomass and respiration rates observed in the Bt and insecticide-applied soils compared to non-Bt soils does allay concerns that either the Bt protein or the tefluthrin typically used to control the corn rootworm reduce microbial biomass or its respiratory activity in field soils. Similarly, the higher N mineralization potential and nitrification rates observed in some soil samples from the Bt and tefluthrin-treated plots indicate higher activity of N-mineralizing microorganisms, a potentially positive consequence as both ammonium and nitrate are effective N sources for maize during grain filling. Our data suggest that cropping MON863 Bt maize is unlikely to adversely affect soil ecology in the short term. Longer-term monitoring of transgenic cropping systems should assure that the biotic functioning of the soil is maintained as a part of studies on overall ecosystem integrity.     

Controlled irrigation and drainage of a rice paddy field reduced global warming potential of its gas emissions

The effect of controlled drainage on methane (CH₄) and nitrous oxide (N₂O) emissions from a paddy field under controlled irrigation (CI) was investigated by controlling the sub-surface drainage percolation rate with a lysimeter. CI technology is one of the major water-saving irrigation methods for rice growing in China. Water percolation rates were adjusted to three values (2, 5, and 8 mm d^?1) in the study. On the one hand, the CH₄ emission flux and total CH₄ emission from paddy fields under CI decreased with the increase of percolation rates. Total CH₄ emissions during the growth stage of rice were 1.83, 1.16, and 1.05 g m^?2 in the 2, 5, and 8 mm d^?1 plots, respectively. On the other hand, the N₂O emission flux and total N₂O emissions from paddy fields under CI increased with the increase of percolation rates. Total N₂O emissions during the growth stage of rice were 0.304, 0.367, and 0.480 g m^?2 in the 2, 5, and 8 mm d^?1 plots, respectively. The seasonal carbon dioxide (CO₂) equivalent of CH₄ and N₂O emissions from paddy fields under CI was lowest in the 2 mm d^?1 plot (1364 kg CO₂ ha^?1). This value was 1.4% and 19.4% lower compared with that in the 5 and 8 mm d^?1 plots, respectively. The joint application of CI and controlled drainage may be an effective mitigation strategy for reducing the carbon dioxide equivalents of CH₄ and N₂O emissions from paddy fields.