No abstract

Natural farming (NF), an environmentally friendly agricultural practice similar to organic farming, was developed in Japan. Unlike conventional farming, little is known about the influence of NF on soil microbial communities, especially the surface soil. We therefore compared the effect of seven years’ conventional practice (CP), conventional practice without chemicals (CF), and NF on soil properties and microbial community structure at two soil depths (0–10, 10–20 cm) in an experimental cabbage field. Both soil depth and agricultural practice significantly influenced edaphic measures and microbial community structure. NF improved bulk density, pH, electrical conductivity, urease activity, and nitrate reductase activity in topsoil; similar trends were observed in deeper soil. Pyrosequencing demonstrated that the use of pesticides in conventional farming (CP) led to lower microbial abundance and diversity in topsoil than CF. Similarly, NF increased microbial abundance compared to CP. However, distinct taxa were present in the topsoil, but not deeper soil, in each treatment. CP-enriched microbial genera may be related to plant pathogens (e.g., Erwinia and Brenneria) and xenobiotic degraders (e.g., Sphingobacterium and Comamonas). The microbial community structure of NF was distinct to CP/CF, with enrichment of Pedomicrobium and Solirubrobacter, which may prefer stable soil conditions. Network analysis of dominant genera confirmed the more stable, complex microbial network structure of the 0–10 cm than 10–20 cm layer. Flavisolibacter/Candidatus Solibacter and Candidatus Nitrososphaera/Leuconostoc are potentially fundamental taxa in the 0–10 cm and 10–20 cm layer networks, respectively. Overall, we show that NF positively affects soil quality and microbial community composition within sustainable farming systems.

Concerns about the soil salinity caused by excessive fertilization have prompted scientists to clarify the detailed mechanisms and find techniques to alleviate the damage caused by this kind of soil salinity. Aims of this study were to elucidate the effect of soil salinity caused by nitrate fertilization and the differences in salinity effect between nitrate salts and NaCl salt with analyses at various levels of crop physiology and molecular biology. A microbial inoculation was also tried to verify whether it could alleviate the salinity-induced loss and damages. In three experiments (Exp I, II and III), nitrate salts (NS) of Ca(NO 3 ) 2 and KNO 3 were applied to potted tomato plants to simulate the soil salinity caused by fertilization and a microbial inoculant (MI) was applied. Photosynthesis was measured using Li-6400. Osmotic adjustment was analyzed using the mathematically modeled pressure-volume curve; O 2 concentration and activity of SOD and nitrate reductase were measured.Expression of nitrate reductase gene and the stress-responsive gene DREB2 was analyzed using the real-time PCR method. In Exp I and II, where the applied NS amount was moderate, NS application at low concentration induced increases in O 2 and MDA concentrations and plants acclimated to the soil salinity as the treatment prolonged for weeks. The acclimation was contributed by osmotic adjustment, activation of SOD and re-compartmentation of cell water between symplasm and apoplasm. These adjustments might be ultimately attributed to up-regulation of stress-responsive genes such as DREB2 as well as the nitrate reductase (NR) gene. However, in Exp III, applications of NaCl and NS at high concentration could not show positive effects as NS did. Application of MI synergistically increased the xerophytophysiological regulation caused by NS and alleviated the salinity damage in addition to its own positive effects on the tomato plants. Different from NaCl, nitrate salts at low application rate increased the total biomass and fruit yield of tomato and induced up-regulation expression of stress-responsive genes and the consequent active osmotic adjustment. However, nitrate application at high level negatively affected tomato plants irrespective of the gene up-regulations. Application of MI alleviated the salinity damage and synergistically increased the xerophytophysiological regulation caused by the soil salinity in addition to its positive effects on the tomato crop but the detailed mechanisms needed to be clarified in future further studies.

No abstract

Nature farming is a farming system that entails cultivating crops without using chemical fertilizers and pesticides. The present study investigated the bacterial and fungal communities in the rhizosphere of soybean grown in conventional and nature farming soils using wild-type and non-nodulating mutant soybean. The effect of soil fumigant was also analyzed to reveal its perturbation of microbial communities and subsequent effects on the growth of soybean. Overall, the wild-type soybean exhibited a better growth index compared to mutant soybean and especially in nature farming. Nodulation and arbuscular mycorrhiza (AM) fungi colonization were higher in plants under nature farming than in conventionally managed soil; however, fumigation drastically affected these symbioses with greater impacts on plants in nature farming soil. The rhizosphere microbiome diversity in nature farming was higher than that in conventional farming for both cultivars. However, the diversity was significantly decreased after fumigation treatment with a greater impact on nature farming. Principal coordinate analysis revealed that nature farming and conventional farming soil harbored distinct microbial communities and that soil fumigation significantly altered the communities in nature farming soils but not in conventional farming soils. Intriguingly, some beneficial microbial taxa related to plant growth and health, including Rhizobium, Streptomyces, and Burkholderia, were found as distinct microbes in the nature farming soil but were selectively bleached by fumigant treatment. Network analysis revealed a highly complex microbial network with high taxa connectivity observed under nature farming soil than in conventional soil; however, fumigation strongly broke it. Overall, the results highlighted that nature farming embraced higher microbial diversity and the abundance of beneficial soil microbes with a complex and interconnected network structure, and also demonstrated the underlying resilience of the microbial community to environmental perturbations, which is critical under nature farming where chemical fertilizers and pesticides are not applied.

Bischofia polycarpa (Levl.) Airy Shaw witches'-broom disease is widespread in southern China. Infected trees show symptoms of severely proliferating shoots, reduced leaf size, yellowing and reddening of leaves, and internode shortening. We detected the phytoplasma in diseased tissues by 4′,6-diamidino-2-phenylindole-HCl fluorescence microscopy and polymerase chain reaction using the universal primers P1/ P7. We conducted sequence similarity analyses based on 16S rRNA and 23S rRNA genes, the spacer region between the 16S and 23S rRNA genes (ISR), the partial ribosomal proteinencoding operon (rp), and the elongation factor Tu (tuf) gene of the BiWB phytoplasma. These analyses unanimously showed that the BiWB phytoplasma belongs to the elm yellows group (the 16SrV group). Phylogenetic and computersimulated restriction fragment length polymorphism analyses using the nearly full-length 16S rRNA gene sequence demonstrated that the BiWB phytoplasma is more closely related to the subgroup 16SrV-B than to the other subgroups in 16SrV. It may represent a novel subgroup, designed as 16SrV-H, which is distinct from other subgroups of phytoplasmas in the 16SrV group.

ABSTRACT. Mycoplasma ovipneumoniae, a bacterial species that specifically affects ovine and goat, is the cause of ovine infectious pleuropneumonia. We cloned, sequenced and analyzed heat shock protein 70 (HSP70) (dnaK) gene of M. ovipneumoniae. The full length open reading frame of the M. ovipneumoniae HSP70 gene consists of 1812 nucleotides, with a G+C content of 34.16%, encoding 604 amino acids. Comparative analysis with the HSP70 sequences of 15 Mycoplasma species revealed 59 to 87% DNA sequence identity, with an amino acid sequence identity range of 58 to 94%. M. ovipneumoniae and M. hyopneumoniae shared the highest DNA and amino acid sequence identity (87 and 94%, respectively). Based on phylogenetic analysis, both the DNA and amino acid identities of M. ovipneumoniae with other mycoplasmal HSP70 were correlated with the degree of relationship between the species. HSP70 of Mycoplasma ovipneumoniaeThe C-terminus of the HSP70 was cloned into a bacterial expression vector and expressed in Escherichia coli cells. The recombinant C-terminal portion of HSP70 protein strongly reacted with convalescent sera from M. ovipneumoniae-infected sheep, based on an immunoblotting assay. This indicates that HSP70 is immunogenic in a natural M. ovipneumoniae infection and may be a relevant antigen for vaccine development.

To understand the distribution of the cultivable fungal community in plant tissues from nature farming tomato plants, we sampled plants of seven different tomato cultivars and recovered 1742 fungal isolates from 1895 stem tissues sampled from three sites in Japan. Overall, the isolation frequency was low (3–13%) and the isolation and colonization frequencies did not vary significantly as a function of the cultivar. The fungi were divided into 29 unique operational taxonomic units (OTUs) with 97% ITS gene sequence identity, the majority of which belong to Ascomycota (99.3%). The dominant genera of cultivable endophytic fungi were Fusarium (45.1%), Alternaria (12.8%), Gibberella (12.0%), and Dipodascus (6.8%). The alpha diversity of the fungal endophytes varied among tomato cultivars. Ordination analysis performed to investigate patterns of endophyte community assemblages on the various cultivars revealed that host cultivars had a significant impact on the endophyte community assemblages in all the study sites. Some of the taxa Fusarium, Alternaria, and Penicillium were found on all cultivars, while few were uniquely present in different cultivars. The dominant taxa may be adapted to the particular microecological and physiological conditions present in tomato stems.