Ainin Niswati

Effect of application of rice straw and compost on the community structure of bacteria associated with microcrustaceans in the floodwater of a paddy field microcosm

Abstract A microcosm experiment was conducted to study the effect of the application of rice straw and compost to a soil on the bacterial communities associated with five species of microcrustaceans in the floodwater of paddy fields based on RFLP analysis. PCR products for bacterial 16S rDNA were digested with four restriction endonucleases (Hinf I, Sau3A I, Hae III, EcoR I). The results showed that the RFLP patterns of the bacterial communities were distinctly different among the microcrustaceans, although DNA fragments common to Tanycypris sp., Cypretta sp., and Heterocypris sp. were recognized. Bacterial communities associated with Tanycypris sp. showed the smallest number of fragments among the microcrustaceans studied. Rice straw and compost application exerted a negligible effect on the band patterns from Cypretta sp. and Moina sp., respectively. Cluster analysis and principal component analysis enabled to separate the band patterns into 2 groups with a total of 4 subgroups: I-1. Moina sp., I-2. Mesocyclops sp., II-1. Tanycypris sp. and Cypretta sp., and II-2. Heterocypris sp. The results indicated that the bacterial association with the microcrustaceans was primarily determined by the genus and species of hosts. Effects of rice straw and compost application on the bacterial communities associated with Moina sp. and Cypretta sp. and the duration of flooding on the bacterial communities associated with all the micro crustaceans were also observed, although the effects were not appreciable compared to those of the kind of host microcrustaceans.

Analysis of communities of ammonia oxidizers, methanotrophs, and methanogens associated with microcrustaceans in the floodwater of a rice field microcosm

Abstract Ammonia-oxidizing bacteria (AOB), methanotrophs (MOB), and methanogens that were associated with Moina sp., Mesocyclops sp., Heterocypris sp. in the floodwater of a rice field microcosm were studied by using DGGE and sequence analysis with amoA / pmoA and methanogen-specific primer sets. Only one AOB and two MOB DGGE bands with the same mobility were detected, irrespective of the microcrustaceans. Effect of the incubation period was observed only in the AOB community associated with Moina sp., and an additional AOB clone appeared in the late period of incubation. Sequence analysis of the bands revealed that both of the closest relatives of the AOB clones belonged to uncultured ammonium monooxygenase genes of α-Proteobacteria, while those of the MOB clones to Methylomicrobium buryatense, an uncultured methanotroph bacterium, and Methylococcus capsulatus within type I methanotrophs belonging to γ-Proteobacteria. In contrast, no amplification products of 16S rDNA of the methanogenic archaea were obtained from any of the microcrustacean samples, indicating the absence or very small populations of methanogens.

Comparison of Bacterial Communities Associated with Microcrustaceans from the Floodwater of a Paddy Field Microcosm: Estimation Based on DGGE Pattern and Sequence Analyses

Bacterial communities associated with five kinds of microcrustaceans (Tanycypris sp., Moina sp., Mesocyclops sp., Cypretta sp. and Heterocypris sp.) from the floodwater of a paddy field microcosm were examined by the application of denaturing gradient gel electrophoresis (DGGE) to PCR-amplified 16S rDNA products with universal bacterial primers and by sequencing of characteristic DGGE bands. The number of DGGE bands of the associated bacteria was small, indicating the association of specific bacterial members with the microcrustaceans studied, among which Tanycypris sp. showed the smallest number of bands. Principal component analysis (PCA) demonstrated that the community structure of the associated bacteria could be divided into three groups: Podocopida (Tanycypris sp., Cypretta sp. and Heterocypris sp.), Moina sp. and Mesocyclops sp., and further analysis separated Tanycypris sp. and Heterocypris sp. into different clusters. The duration of the incubation period affected the bacteria associated with Tanycypris sp., Moina sp. and Cypretta sp. only. Nearly all of the associated bacteria belonged to Gram-negative bacteria, especially the Cytophaga-Flavobacterium-Bacteroides (CFB) group. Closest relatives of the DGGE bands common to three Podocopida and Mesocyclops sp. belonged to an invertebrate endosymbiont.

Diversity of Fungi on Decomposing Leaf Litter in a Sugarcane Plantation and Their Response to Tillage Practice and Bagasse Mulching: Implications for Management Effects on Litter Decomposition

To minimize the degradation of soil organic matter (SOM) content in conventional sugarcane cropping, it is important to understand how the fungal community contributes to SOM dynamics during the decomposition of sugarcane leaf litter. However, our knowledge of fungal diversity in tropical agroecosystems is currently limited. Thus, we determined the fungal community structure on decomposing sugarcane leaf litter and their response to different soil management systems using the internal transcribed spacer region 1 (ITS1) amplicon sequencing method afforded by Ion Torrent Personal Genome Machine (PGM). The results indicate that no-tillage had positive effects on the relative abundance of Zygomycota and of some taxa that may prefer a moist environment over conventional tillage, whereas bagasse mulching decreased the richness of operational taxonomic units (OTUs) and had positive effect on the relative abundance of slow-growing taxa, which may prefer poor nutrient substrates. Furthermore, a combination of no-tillage and bagasse mulching increased the abundance of unique OTUs. We suggest that the alteration of fungal communities through the changes in soil management practices produces an effect on litter decomposition.

Bacterial communities associated with aquatic organisms in the floodwater of a Japanese paddy field estimated by RFLP pattern analysis

Abstract Bacterial communities associated with crustacean (Tanycypris, Cladocera, Cyclopoida), Diptera (larvae of Cricotopus sp.), and roots of duckweed (Lemna paucicostata Hegelm) in the floodwater of a paddy field were analyzed based on the RFLP patterns of 16S rDNA. A larger number of RFLP bands was obtained from the bacterial communities in the floodwater and that associated with Cyclopoida than from the bacterial community associated with the other host organisms. The bacterial community associated with Tanycypris gave the smallest number of bands compared with the other habitats. DNA fragments common to Tanycypris, Cladocera, Cyclopoida, and Diptera and specific to the respective organisms were recognized. The RFLP pattern of the bacterial communities in the floodwater was markedly different from and more complex than those from aquatic organisms. The RFLP pattern of the bacterial community associated with Lemna roots was also specific. Cluster analysis and principal component analysis enabled to clearly separate the RFLP patterns of the bacterial communities associated with aquatic organisms from one another. The effect of sampling time on the bacterial communities was not appreciable compared to the effect of host organisms.

Methane emission from Indonesian rice fields with special references to the effects of yearly and seasonal variations, rice variety, soil type and water management

Total amounts of CH 4 emission from a Sumatra rice field were in the ranges 29.5-48.2 and 43.0-64.6 g CH 4 m -2 season -1 for the plots with chemical fertilizer (CF-plot) and those with rice straw application (RS-plot), respectively. Nearly the same amounts of CH 4 were emitted in the first and second half of the growth period, irrespective of rice straw application. The increase in the amounts of CH 4 emission by rice straw application were from 1.3 to 1.6 times. There was no significant difference in the mean CH 4 emission rates between rainy and dry seasons. Rain-fed conditions decreased the CH 4 emission by 27-37% compared with continuously flooded conditions. Total amounts of CH 4 emission from a rice field growing eight popular modern rice varieties in Indonesia were in the ranges 32.6-41.7 and 51.3-64.6 g CH 4 m -2 season -1 for CF-and RS-plots, respectively. Total amounts of CH 4 emission from four Sumatra rice fields with different soil types (a Typic Paleudult, a Typic Sulfaquent, a Typic Tropohumult and a Typic Tropopsament) were in the range 22.1(a Typic Sulfaquent) to 53.4 (a Typic Tropohumult) g CH 4 m -2 season -1 for CF-plots and from 26.7 (a Typic Sulfaquent) to 72.2 (a Typic Tropohumult) g CH 4 m -2 season -1 for RS-plots. CH 4 emission rates from Bali rice fields with soils of volcanic ash origin were very low; 3.5-7.7 and 5.3-14.3 g CH 4 m -2 season -1 for CF- and RS-plots, respectively. Respective rice fields showed the specific productivity of grain production, and CH 4 emission rates for 1 kg grain production were scattered widely from 8-11 and 11.24 g CH 4 kg -1 grain for rice fields of volcanic ash origin to 83 and 121 g CH 4 kg -1 grain for a Sumatra rice field for CF- and RS-plots, respectively. Water management was also an important factor in decreasing the CH 4 emission rate.

Shifts in the composition and potential functions of soil microbial communities responding to a no-tillage practice and bagasse mulching on a sugarcane plantation

This study examined the effect of conversion from a conventional tillage (CT) to a no-tillage (NT) practice and of bagasse mulching (M) on soil microbial community composition and potential functions, using phospholipid fatty acid (PLFA) analysis and shotgun metagenome sequencing. Our results showed that both the NT and the M treatment increased microbial PLFAs. The shotgun sequencing results suggested that the functional profiles are more resistant to agricultural managements than to community compositions, which supports the hypothesis of the functional redundancy of soil microbial communities. However, some metabolism-related sequences were significantly affected by different treatments. The percentage of sequences related to metabolism of carbohydrates, especially saccharide groups, was significantly higher in the CT soils than in NT and M soils, which may be linked to lower carbon (C) availability in CT soils. Compared with CT, the NT had higher alpha diversity and more sequences related to DNA metabolism, which may be associated with higher nutrient availability. On the other hand, the M treatment decreased the percentages of sequences related to the metabolism of amino acids and derivatives, which may be due to the limited nitrogen (N) because of the high C/N ratio of bagasse. We also observed interaction effects of the NT and M treatments; although both the NT and M treatments increased the relative abundance of Proteobacteria, this variable in NT + M soils was not higher than in each single treatment. Overall, our findings suggest that the microbial communities change their composition and functionality in response to the NT and M treatments, and these shifts have the potential to affect important soil processes that sustain crop productivity, such as C sequestration and major nutrient cycles.

Activities of soil enzymes in fields continuously cultivated with cassava, sugarcane, and pineapple in middle terrace areas of Lampung Province, South Sumatra, Indonesia

Abstract Changes in the activities of soil enzymes (acid and alkaline phosphatases, β-glucosidase, and arylsulfatase) associated with continuous cultivation of cassava, sugarcane, and pineapple were studied in middle terrace areas of Lampung Province, South Sumatra, Indonesia. Soil samples were collected from fields continuously cultivated with cassava for the period ranging from 0 to 10 y, with sugarcane from 0 to 20 y, and with pineapple from 0 to 10 y. Continuous cultivation did not show conspicuous effects on soil pH, and contents of total N, organic C, and available P as well as soil enzymatic activities. However, the changes in the activities of the soil enzymes generally showed a significant relationship with the contents of soil organic C and total N.

Effect of Application of Rice Straw and Compost on the Bacterial Communities Associated with Moina sp. in the Floodwater of a Paddy Soil Microcosm: Estimation Based on DGGE Pattern and Sequence Analyses

Bacterial communities associated with Moina sp. in the floodwater of a paddy field microcosm were examined by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rDNA. Eighteen out of 20 eubacterial DGGE bands were sequenced. The associated eubacterial communities mainly consisted of the Cytophaga-Flavobacterium-Bacteroides group and α-, β-, and γ-Proteobacterial groups, irrespective of the application of rice straw and rice straw compost. The effect of the application of rice straw and compost on the communities was not appreciable, compared with host specificity. An uncultured Cytophagales bacterium was estimated to be specifically associated with Moina sp. Presence of bacteria that are specific to rice straw treatment was also estimated.

The Effects of Nitrogen Fertilizer on Soil Microbial Communities Under Conventional and Conservation Agricultural Managements in a Tropical Clay-rich Ultisol

Abstract The response of microbial communities to N fertilizer varies depending on environmental and management-related factors. However, few studies have compared the effects of N fertilization on microbial communities under different agricultural management. We thus compared the biomass and composition of microbial communities in N-fertilized and unfertilized long-term (25 years) fields managed under conventional tillage with crop residue removal (CTR) and no-tillage with crop residue mulch (NTM) systems. Soil samples were taken in January 2011 and July 2012 at a depth of 0 to 10 cm, and phospholipid fatty acid (PLFA) profiles were measured. Fungal abundance was lower in N-fertilized soils than in unfertilized soils under both management systems at both sampling times. Bacterial abundance was lower in N-fertilized soils than in unfertilized soils under the CTR system, whereas no difference was observed between N-fertilized and unfertilized soils under the NTM system in January 2011. However, in July 2012, bacterial abundance was lower in N-fertilized soils than in unfertilized soils under both management systems. Principal component analysis of the PLFA profiles showed that N fertilizer had a significant effect on the PLFA composition under the CTR system but had less impact under the NTM system. These results suggest that (i) fungal biomass is negatively affected by N fertilizer regardless of management system; (ii) bacterial response to N fertilizer differs temporally between management systems, reflecting temporal changes in soil C content; and (iii) the NTM system mitigates N effects on the composition of soil microbial communities.