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1.
Junjie Liu Guanghua Wang Chunyu Zheng Xiaohui Yuan Xiaobing Liu 《Soil biology & biochemistry》2011,43(9):1980-1984
We surveyed the major capsid genes (g23) of T4-type bacteriophages using the primers MZIA1bis and MZIA6 and DNA extracted from seven upland black soils in Northeast China. In total, 99 different g23 clones were obtained. Approximately half of the clones fell into paddy groups, whereas the rest belonged to one of several groups containing only clones from upland black soils or remained ungrouped, suggesting that the T4-type phage communities in the upland black soil were relatively similar to those in paddy field soils but that specific communities exclusively inhabit the upland black soil. UniFrac analysis of all of the g23 clones obtained from various environments indicated that the T4-type phage communities varied among marine, lake, paddy field soil and upland soil environments and that the T4-type phage communities in upland black soils varied by sampling location. 相似文献
2.
Guanghua Wang Jun Murase Katsutoshi Taki Yoshinori Ohashi Nanako Yoshikawa Susumu Asakawa Makoto Kimura 《Biology and Fertility of Soils》2009,45(5):521-529
Although microbial communities in soil are well known to change with soil depth, the changes in viral communities with soil
depth have not been documented. This study examined the soil depth profiles of T4-type phage communities in two Japanese rice
fields from g23 clones in soil DNA extracts to a depth of 1 m. T4-type phage communities changed with soil depth, and the communities were
grouped into two groups: the communities of the surface soil layers, where rice roots developed densely, and those of the
subsoil layers. Although coarse- and fine-textured soils were stratified in the subsoil layers in both profiles, denaturing
gradient gel electrophoresis band patterns and phylogenetic affiliation of g23 were highly similar to each other among the subsoil layers in both fields, indicating that soil texture did not affect T4-type
phage communities in these fields. In addition, some clones had g23 sequences identical to those retrieved from rice fields in Northeast China, indicating that closely related viruses and their
hosts distribute across the sea between rice fields in Japan and Northeast China. 相似文献
3.
Vita Ratri CAHYANI Jun MURASE Eiji ISHIBASHI Susumu ASAKAWA Makoto KIMURA 《Soil Science and Plant Nutrition》2009,55(2):264-270
The present study compared the capsid gene ( g23 ) of T4-type bacteriophages (phages) in Mn nodules with those in the plow layer soil and subsoils of two Japanese paddy fields by applying the primers MZIA1bis and MZIA6 to DNA extracts from the nodules and soils. The deduced amino acid sequences of the g23 genes in the Mn nodules were similar to those in the plow layer soil and in the subsoils. This result indicated that similar T4-type phage communities developed at these sites and that the diversity of T4-type phage communities was wide enough to cover those in the plow layer soil and in the subsoils. The majority of g23 clones formed several clusters with the clones and phages obtained from far-apart paddy fields, and the sequences of two clones were completely identical to a phage and a clone from other paddy fields at the nucleotide or amino acid level, indicating horizontal transfer of g23 genes between those paddy fields. A clone with a long nucleotide residue (686 bp) and a distribution remote from the other clones in the phylogenetic tree indicated that there were many uncharacterized, novel g23 genes in the paddy fields. 相似文献
4.
Junjie Liu Zhenhua Yu Xinzhen Wang Jian Jin Xiaobing Liu 《Soil Science and Plant Nutrition》2016,62(2):133-139
Our previous study revealed the high diversity of the major capsid gene (g23) of T4-type phages that existed in the paddy field soils in Northeast China. In this study, the phylogeny and genetic diversity of the g23 gene in the paddy floodwater samples collected from five sampling sites at three sampling times during the rice (Oryza sativa L.) growth season in Northeast China are reported. In total, 104 different g23 clones were isolated, among which 50% of the clones exhibited the highest identities with the clones retrieved in paddy soils and upland black soils. The remaining clones had the highest identities with lake origins. Phylogenetic analysis revealed that 43% of the g23 clones grouped into three novel subgroups which included the clones unique to paddy floodwater, and no g23 sequences obtained in paddy floodwater fell into the paddy soil groups II, III, IV, V, VI, VII and NPC-A. UniFrac analysis of g23 clone assemblages demonstrated that T4-type phage communities in paddy floodwater were changed spatially and temporally, and the communities were different from those in paddy soils. Further comparison of the g23 clone assemblages from different environments demonstrated that T4-type phages were biogeographically distributed, and the distribution was both affected by geographical separation and ecological processes across the biomes. 相似文献
5.
Takeshi Fujii Natsuko Nakayama Mizuhiko Nishida Hiroyuki Sekiya Naoto Kato Susumu Asakawa Makoto Kimura 《Soil biology & biochemistry》2008,40(5):1049-1058
Viruses exist everywhere on the planet. Recent development in viral genomics confirmed that genomic information is preserved among viral subsets and can be used for phylogenetic classification of viruses and for evaluation of viral diversity in the environment. The capsid gene of T4-type bacteriophages, g23, is the most widely applied gene for evaluating the diversity of the T4-type bacteriophage family. In this study, we applied denaturing gradient gel electrophoresis to PCR products of DNA with g23-specific primers that were extracted from a Japanese paddy field under long-term fertilizer trial and obtained 39 different g23 clones at the DNA level. They showed identities of 27–99% with the clones within the NCBI database at the amino acid level. They were quite distinctive from those obtained in marine environments and most of them formed six phylogenetically novel groups in the T4-type bacteriophage family with the clones obtained from another paddy field. The existence of six novel groups was confirmed from molecular analysis of all the amino acid sequences between the primers, of the amino acid sequences excluding hypervariable region, and of those of conserved regions. These findings indicate that T4-type bacteriophage communities in paddy fields consist of previously uncharacterized members phylogenetically distant from those in marine environments. The type of fertilizers and the stage during rice cultivation were not the major factors in determining T4-type bacteriophage communities in the paddy field. 相似文献
6.
Guanghua Wang Motoki Hayashi Kazunari Tsuchiya Makoto Kimura 《Soil biology & biochemistry》2009,41(1):13-20
Many studies have shown the ecological importance of viruses as the greatest genomic reservoirs on the planet. As bacteriophages (phages) comprise the majority of viruses in the environment, we surveyed the capsid genes (g23) of T4-type phages, Myoviridae, from DNA extracts of three paddy field soils located in northern, central and southern Japan using the degenerate primers MZIA1bis and MZIA6. Denaturing gradient gel electrophoresis (DGGE) was performed to separate PCR-amplified g23 products, and 56 DGGE bands were identified as g23 fragments. Only nine clones were grouped into T-evens, PseudoT-evens and ExoT-evens, and most of the other clones were classified into Paddy Groups I-VI. No significantly different distribution of g23 clones was observed among the paddy fields at the group level, indicating that phage communities estimated from the g23 composition were common on the nationwide level. Comparison of g23 sequences showed that g23 genes in paddy fields were different from those in marine environments, and more divergence of g23 genes was estimated in the paddy fields compared to the marine environment. Two novel g23 clones with very short amino acid residues were detected, suggesting the existence of uncharacterized, novel groups of g23 genes in paddy field soils. 相似文献
7.
Vita Ratri CAHYANI Jun MURASE Susumu ASAKAWA Makoto KIMURA 《Soil Science and Plant Nutrition》2009,55(4):468-477
The present study examined T4-type phage communities in rice straw (RS) under the composting process by analyzing the composition of the major capsid gene ( g23 ) of T4-type bacteriophages. The g23 clones were obtained from RS throughout the composting process from RS materials to composting RS in the curing stage (for 124 days). Most of the g23 clones were phylogenetically closely related to those in rice field soils and rice field floodwaters, and Paddy Groups II and III appeared to characterize the g23 genes in the composting RS. The diversity of g23 genes in the composting RS was highest in the RS material (day 0 after the onset of composting) and in the early thermophilic stage (day 7), and decreased markedly in the middle and curing stages. This change was in contrast to that of the bacterial community, which showed higher diversity in the middle and curing stages. There was no specific clone that characterized any stage during the composting process. These findings indicate that the phage community is not the major controlling agent in determining eubacterial succession and that the thermophilic stage in the composting process efficiently annihilated T4-type phages in the composting pile. 相似文献
8.
We surveyed the capsid genes (g23) of T4-type bacteriophages in DNA extracted from fifteen rice field soils in Northeast China using primers MZIA1bis and MZIA6. Denaturing gradient gel electrophoresis (DGGE) was performed to separate PCR-amplified g23 products. In total, 53 DGGE bands were identified as g23 clones, nine of which belonged to a novel, Northeast China-specific group. In addition, four and six clones formed two novel groups with previously ungrouped clones obtained from Japanese rice fields. The majority of the remaining clones fell into Paddy Groups I and V, none of the clones belonged to Paddy Groups II, III, IV, and VI, indicating that phylogenetic distribution of g23 genes in rice fields in Northeast China was different from that in Japanese rice fields. 相似文献
9.
《Soil Science and Plant Nutrition》2013,59(4):468-477
Abstract The present study examined T4-type phage communities in rice straw (RS) under the composting process by analyzing the composition of the major capsid gene (g23) of T4-type bacteriophages. The g23 clones were obtained from RS throughout the composting process from RS materials to composting RS in the curing stage (for 124?days). Most of the g23 clones were phylogenetically closely related to those in rice field soils and rice field floodwaters, and Paddy Groups II and III appeared to characterize the g23 genes in the composting RS. The diversity of g23 genes in the composting RS was highest in the RS material (day 0 after the onset of composting) and in the early thermophilic stage (day 7), and decreased markedly in the middle and curing stages. This change was in contrast to that of the bacterial community, which showed higher diversity in the middle and curing stages. There was no specific clone that characterized any stage during the composting process. These findings indicate that the phage community is not the major controlling agent in determining eubacterial succession and that the thermophilic stage in the composting process efficiently annihilated T4-type phages in the composting pile. 相似文献
10.
Guanghua Wang Jun Murase Susumu Asakawa Makoto Kimura 《Biology and Fertility of Soils》2010,46(2):93-102
In order to evaluate the genetic diversity of cyanophage communities of rice fields, viral capsid assembly protein gene (g20) was amplified with primers CPS1 and CPS8. The DNA was extracted three times from viral concentrates obtained from floodwater
samples collected in each of four different plots (no fertilizer; P and K chemical fertilizers; N, P, and K chemical fertilizers;
and chemical fertilizers with compost). Denaturing gradient gel electrophoresis (DGGE) gave different g20 clones. The sequencing of DGGE bands revealed that the g20 genes of the floodwater were divergent and that the majority of clones formed several unique groups. However, they were more
closely related to g20 sequences from freshwaters than to those from marine waters, suggesting that g20 genes in terrestrial aquatic environments are different from those in marine environments. 相似文献
11.
Our previous study indicated that the diversity of the major capsid gene (g23) of T4-type bacteriophages (phages) of Novosphingobium and Sphingomonas strains isolated from the floodwater of a Japanese paddy field is comparable to those of the clones obtained from other Japanese paddy fields. For more strict comparison of the diversity, this study examined g23 sequences between Novosphingobium and Sphingomonas phages and phage communities in the identical floodwater of a Japanese paddy field. The clones were obtained by applying g23-specific primers to DNA extracted from the floodwaters. Many 23 clones in the floodwater were grouped into the same clusters of Paddy Groups I-VI with g23 genes of Novosphingobium/Sphingomonas phages with some clones belonging to an additional cluster. In addition, the remaining clones belonged to the clusters of marine clones and T4-type enterophages. These findings indicate that the g23 genes in the floodwater are more diversified than those of Novosphingobium/Sphingomonas phages including g23 genes closely related to the genes of enterophages and marine origins. 相似文献
12.
Soil purple phototrophic bacterial (PPB) communities and their responses to elevated atmospheric carbon dioxide (CO2) concentration and nitrogen (N) fertilizer were investigated under a rotation of paddy rice (Oryza sativa L.) and winter wheat (Triticum aestivum L. cv. Yangmai 14) cultivation in a FACE (free‐air CO2 enrichment) system. Community structures and abundances of PPB were determined by denaturing gradient gel electrophoresis (DGGE) and real‐time quantitative PCR respectively, targeting the pufM gene, which encodes a protein in the light reaction centre of PPB. Soil PPB communities were more diverse and larger under rice than under wheat cultivation, which may be attributed to the flooding of the paddy field and soil moisture changes. Elevated atmospheric CO2 concentration significantly increased the abundance and biodiversity of PPB in soils under rice cultivation, while N fertilizer application rate had less effect on the abundance and diversity. Phylogenetic analysis showed that two common dominant DGGE bands belonged to Bradyrhizobium‐ and Rhodopseudomonas palustris‐like PPB in both rice and wheat soils. The results demonstrated a significant shift in soil PPB communities during the rice‐wheat rotation, and a strong positive response of PPB communities to an elevated atmospheric CO2 concentration. Our results also indicated that a diverse and abundant soil PPB community could occur in upland crop fields as well as in aquatic environments and paddy‐rice fields. These findings extend our understanding of the ecological significance of PPB in terrestrial soil environments and their responses to future climate change. 相似文献
13.
Xiaojing HU Junjie LIU Dan WEI Ping ZHU Xi'an CUI Baoku ZHOU Xueli CHEN Jian JIN Xiaobing LIU Guanghua WANG 《土壤圈》2020,30(1):73-86
Denitrification is one of the major processes causing nitrogen loss from arable soils.This study aimed to investigate the responses of nir S-type denitrifier communities to different chronic fertilization regimes across the black soil region of Northeast China.Soil samples were collected from sites located in the north(NB),middle(MB),and south(SB)of the black soil region of Northeast China,each with four chronic fertilization regimes:no fertilizer(No F),chemical fertilizer(CF),manure(M),and chemical fertilizer plus manure(CFM).Methods of quantitative polymerase chain reaction(q PCR)and Illumina Mi Seq sequencing were applied to assess the abundance and composition of denitrifier communities by targeting the nir S gene.The results showed that the M and CFM regimes significantly increased the abundances of nir S-type denitrifiers compared with No F at the three locations.The majority of nir S sequences were grouped as unclassified denitrifiers,and the different fertilizers induced little variation in the relative abundance of known nir S-type denitrifier taxa.Over 90%of the sequences were shared among the four fertilization regimes at each location,but none of the abundant operational taxonomic units(OTUs)were shared among the three locations.Principal coordinate analysis(PCo A)revealed that the communities of nir S-type denitrifier were separated into three groups that corresponded with their locations.Although similar fertilization regimes did not induce consistent changes in the nir S-type denitrifier communities,soil p H and NO-3-N content simultaneously and significantly influenced the structure of nir S-type denitrifier communities at the three locations.Our results highlight that geographical separation rather than chronic fertilization was the dominant factor determining the nir S-type denitrifier community structures,and similar chronic fertilization regimes did not induce consistent shifts of nir S-type denitrifier communities in the black soils. 相似文献
14.
Intensive cropping, especially of rice, is considered to contribute to negative effects not only on soil chemical and biological
properties but also on long-term grain yield. Appropriate crop rotation is often practiced as an alternative strategy to overcome
the negative side effects of intensive cropping. Although soil microbial diversity and community structure have been shown
to respond differently to altered agricultural management practices, little is known about possible links between crop rotation
and grain yield on bacterial communities in rice paddy soil. In this study, we investigated the impact of specific rotational
crops and compared it with intensive rice cultivation. The main crop rice (Oryza sativa) was rotated with maize (Zea mays) and mungbean (Phaseolus aureus) in different combinations in a system cultivating three crops per year. Soil bacterial communities were studied in two different
cropping periods using pyrosequencing of the variable V4 region of the 16S rRNA. Our results showed that rotation with alternative
crops increased rice yield by 24–46% depending on rotation structure and that bacterial community structure was altered in
the presence of mungbean and/or maize compared to that in rice monoculture. In the crop rotation systems, composition, abundance,
and diversity of soil bacterial communities were significantly different and higher than those in rice monoculture. Our results
show that effects of crop rotation relate to changes in soil bacterial community structure suggesting that appropriate crop
rotations provide a feasible practice to maintain the equilibrium in soil microbial environment for sustainable rice cultivation. 相似文献
15.
长期施肥红壤性稻田和旱地土壤有机碳积累差异 总被引：1，自引：1，他引：0
16.
Cho Cho Tun Makoto Ikenaga Susumu Asakawa Makoto Kimura 《Soil Science and Plant Nutrition》2013,59(6):805-813
Rice straw including leaf sheaths and blades put in nylon mesh bags was placed in the plow layer of a Japanese paddy field after harvest under upland conditions and after transplanting of rice seedlings under flooded conditions. In addition, rice straw that was decomposed under the upland conditions during the off-crop season in winter was placed again in soil at the time of transplanting. The materials were collected periodically to analyze the community structure of the bacteria and fungi responsible for rice straw decomposition by PCR-RFLP analysis. The PCR products with 27f and 1492r primers designed for bacterial 16S rDNA and with EF3 and EF4 primers designed for fungal 18S rDNA were digested with four restriction endonucleases (Hinf I, Sau3A I, Hae III, EeoR I). Bacterial communities in the decomposing rice straw were different from each other between upland and flooded conditions, between leaf sheaths and blades, and between straw samples with and without decomposition under upland conditions during the off-crop season. Fungal communities in the decomposing rice straw were also different between the leaf sheaths and blades under upland soil conditions. Score plots of bacterial and fungal communities in the principal component analysis were separated from the plot of the straw materials along with the duration of the placement, indicating the succession of bacterial and fungal communities in decomposing rice straw with time. 相似文献
17.
Diversity of methanogenic archaeal communities in Japanese paddy field ecosystem was evaluated by the denaturing gradient
gel electrophoresis (DGGE) after PCR amplification of the 16S rRNA genes (16S rDNAs), sequencing analysis and data evaluation
by principal component analysis. Data were obtained from samples collected from the plowed soil layer, rice roots, rice straws
incorporated in soil, plant residues (mixture of weeds, rice litters, rice roots, and rice stubbles) in soil, and composing
rice straw. The number of bands of DGGE profiles ranged from 12 to 26 with the highest numbers in rice roots and rice straws
incorporated in soil. However, the diversity indices based on both the numbers and intensity of bands indicated that the community
of the plowed soil layer was the most diverse, even, and stable. Sequencing of the main DGGE bands showed the presence of
Methanomicrobiales, Methanosarcinales, Methanobacteriaceae, and Methanocellales. The plowed soil layer included all phylogenetic groups of the methanogenic archaea of the other studied habitats, with prevalence
of the members of Methanomicrobiales and Methanocellales. The phylogenetic diversity was compared with that of paddy soils collected in Italy, China, and the Philippines and that
of 12 anaerobic environments (fen, waste, coast, permafrost, natural gas field, bovine rumen, riparian soil, termite, ciliate
endosymboints, lake sediment, landfill, and seep rumen). The phylogenetic diversity was more similar among paddy soils than
with the other anaerobic environments. Probably, the methanogenic archaeal communities of the paddy field soils were characterized
by indigenous members and some of the members of the community of the plowed soil layer colonized rice roots, rice straws,
and plant residues. 相似文献
18.
《Applied soil ecology》2005,28(2):147-162
In the EU, municipal sewage sludge application to agricultural land has increased dramatically since the ban on dumping at sea came into effect in 1998. There are many concerns related to potential contamination and reduction in plant productivity. In this study, the aim was to assess the impact of repeated long-term soil amendment with anaerobically digested sewage sludge on methanogen diversity in an upland soil ecosystem. Sludge-treated and untreated upland soil samples as well as samples of the sludge used, were analysed for the diversity of methanogens using TGGE, PCR-RFLP and DNA sequence analysis of approximately 490 bp of the mcrA operon. PCR analysis using mcrA specific oligonucleotide primers confirmed the presence of methanogen DNA in treated and untreated soil samples and in sewage sludge. TGGE was used to describe the diversity of methanogen mcrA sequences and the differences in community structure between samples. Ninety-six mcrA gene PCR products were screened using RFLP analysis representing methanogen DNA amplified from anaerobically digested sewage sludge, control soils and sludge treated soils. Fourteen RFP's were detected in all treatments, five of which were common to all three treatments. Thirty-eight cloned amplimers were selected for sequencing and phylogenetic analysis. These included representatives of each RFP. From control soils, sludge and sludged soil samples 15, 16 and 7 clones were sequenced, respectively. Phylogenetic analysis suggested that they represented hitherto uncharacterised mcr genes; 35 of the clones fell into 7 clusters supported by moderate to high bootstrap values. The diversity of methanogens in an upland soil (treated and untreated) and sludge was evaluated and marked differences in the diversity of the methanogen communities was observed between the treatments. Our results indicate that sludge application may reduce soil methanogen community diversity. 相似文献
19.
Effects of biochar addition on N<Subscript>2</Subscript>O and CO<Subscript>2</Subscript> emissions from two paddy soils 总被引：2，自引：0，他引：2
Jinyang Wang Man Zhang Zhengqin Xiong Pingli Liu Genxing Pan 《Biology and Fertility of Soils》2011,47(8):887-896
Impacts of biochar addition on nitrous oxide (N2O) and carbon dioxide (CO2) emissions from paddy soils are not well documented. Here, we have hypothesized that N2O emissions from paddy soils could be depressed by biochar incorporation during the upland crop season without any effect
on CO2 emissions. Therefore, we have carried out the 60-day aerobic incubation experiment to investigate the influences of rice
husk biochar incorporation (50 t ha−1) into two typical paddy soils with or without nitrogen (N) fertilizer on N2O and CO2 evolution from soil. Biochar addition significantly decreased N2O emissions during the 60-day period by 73.1% as an average value while the inhibition ranged from 51.4% to 93.5% (P < 0.05–0.01) in terms of cumulative emissions. Significant interactions were observed between biochar, N fertilizer, and
soil type indicating that the effect of biochar addition on N2O emissions was influenced by soil type. Moreover, biochar addition did not increase CO2 emissions from both paddy soils (P > 0.05) in terms of cumulative emissions. Therefore, biochar can be added to paddy fields during the upland crop growing
season to mitigate N2O evolution and thus global warming. 相似文献
20.
There are increasing concerns on the environmental impacts of intensive chemical agriculture.The effect of high agrochemical inputs used in intensive chemical farming was assessed on soil microbiological,molecular and biochemical properties in tropical Vertisols in India.Farm field sites under normal cultivation of arable crops using high inputs of fertilizers and pesticides in chili(Capsicum annum L.,5.0× dose for fertilizers and 1.5× dose for pesticides over normal inputs) and black gram(Vigna mungo L.Hepper,2.2x dose for fertilizers and 2.3× dose for pesticides over normal inputs) were compared with adjacent sites using normal recommended doses.Organic carbon and basal respiration showed no response to high inputs of fertilizers and pesticides in soils of both crops.Labile carbon decreased by 10% in chili soils and increased by 24% in black gram soils under high input farming system.The proportion of soil labile carbon as a fraction of soil organic carbon was unaffected by high inputs.The labile carbon mineralization coefficient(qM_(LC)) increased by 50.0% in chili soils,indicating that the soil microorganisms were under stress due to high agochemical inputs,whereas qM_(LC) decreased by 36.4% in black gram soils.Copiotrophs increased due to high inputs in soils of both chili(63.1%) and black gram(47.1%).Oligotrophs increased by 10.8% in black gram soils but not in chili soils.The abundance of amoA gene reduced by 39.3% in chili soils due to high inputs and increased significantly by 110.8% in black gram soils.β-Glucosidase also increased by 27.2% and 325.0%,respectively.Acid phosphatase activity reduced by 29.2% due to high inputs in chili soils and increased by 105.0% in black gram soils.The use of high agrochemical inputs thus had adverse consequences on biological health in chili but not in black gram soils.In soils cultivated with black gram,the moderating effect of cultivating legumes and their beneficial effect on soil health were evident from the increase in soil labile carbon,lower qM_(LC),higher amoA gene and enzyme activities.Overall results showed that cultivation of legumes permits intensive chemical farming without deteriorating soil biological health. 相似文献