Accumulation of free oxyhydroxides in termite (Macrotermes bellicosus (Smeathman)) mounds and the implications for their dynamics in an African savannah Ultisol

The present study aimed to assess the dynamics of oxyhydroxides via termite mounds in a tropical savannah of Central Nigeria, where the soils often contain oxyhydroxides as a major component of soil minerals. To this end, the quantities of oxyhydroxides stored in mounds built by Macrotermes bellicosus (Smeathman) were compared to those stored in surface (Ap1) soils, and their turnover rates were estimated. Both the mound wall and nest of M. bellicosus were enriched two- to 10-fold with acidified ammonium oxalate soluble iron (Fe_o) and aluminum (Al_o) and dithionite-citrate-bicarbonate (DCB) soluble iron (Fe_d) and aluminum (Al_d) relative to the adjacent surface soil horizon. These oxyhydroxide contents were positively correlated with the clay content (P < 0.05), suggesting that M. bellicosus preferentially used silicate clay-associated oxyhydroxides for mound construction. The Fe_d, Al_d and DCB-soluble manganese (Mn_d) preserved in the M. bellicosus mounds ran up to 112 ± 25.6, 5.72 ± 1.41 and 2.17 ± 0.68 kg ha^?1, accounting for 1.91 ± 0.23%, 1.00 ± 0.60% and 0.35 ± 0.09% of the total amount stored in the surface soil horizon, respectively. Furthermore, the estimated turnover rates of Fe_d, Al_d and Mn_d were 6.6, 0.33 and 0.14 kg ha^?1 year^?1, respectively. These findings suggest that the mound-building termites significantly impacted the dynamics of free oxyhydroxides in an African savannah soil.     

Effects of anti-auxins on secondary aerenchyma formation in flooded soybean hypocotyls

In flooded hypocotyl of soybean (Glycine max), cell division in phellogen and the elongation of these cells are enhanced, and thereby a secondary aerenchyma with high porosity is produced. Auxin controls cell division and cell elongation in many plants, so we studied its role in secondary aerenchyma development. Soybean plants with fully expanded unifoliolate leaves were flooded for 6 d with solutions (100 μM each) of seven anti-auxins. TIBA, NPA, HFCA, 1-NOA, or CHPAA did not restrict the secondary aerenchyma formation, while MH moderately suppressed the aerenchyma development, and PCIB strongly inhibited the development of phellogen and secondary aerenchyma. However, the endogenous IAA concentrations in the flooded hypocotyls did not increase or decrease relative to the controls until 72 h, when a secondary aerenchyma was observed. From these results, it is unclear whether auxin plays an important role in the process of secondary aerenchyma formation under flooding.     

Bird responses to broad-leaved forest patch area in a plantation landscape across seasons

Although plantation forests have widely replaced native forests worldwide, few studies have examined the effects of plantation forestry on organisms at the landscape level. In this study, we examined the effects of broad-leaved forest patch area (1.4–312 ha) on bird assemblages in a conifer plantation-dominated landscape during wintering and breeding seasons. We also surveyed birds in the plantation matrix and treated the patch area of the matrix as 0. We examined whether the detection rates of species changed suddenly across patch area (threshold) using segmented regression. We found that species richness increased with patch area in both seasons. Responses of detection rates to patch area varied and were categorized as follows: insensitive, linear increase and decrease, quadratic increase and decrease, concave and convex. Thresholds indicating that the detection rate suddenly increased above a certain patch area were found for two species only in the winter. Species responses varied more in the winter than in the breeding season. Certain ecological traits of species were consistently associated with the responses to patch area across seasons (migratory strategy, nesting substrate and foraging trait), while body weight was only associated in the winter. Because species richness and detection rates of many species were high in large patches, large broad-leaved forests (especially >40 ha) should be retained and restored with high priority. Additionally, bird responses to patch area in the winter should not be ignored because many species required large patches during the winter season.     

Morphology, host range and phylogenetic diversity of Sphingomonas phages in the floodwater of a Japanese paddy field

Members of the Sphingomonas -related genera ( Sphingomonas , Sphingobium , Novosphingobium and Sphingopyxis ) are dominant in bacterial isolates from the floodwater of Japanese paddy fields. Fifty-eight Sphingomonas / Novosphingobium bacteriophages (phages) were isolated to elucidate their morphology, host range and phylogenetic diversity based on the capsid gene ( g23 ) sequence. All of the phages were siphoviruses with isometric or elongated, icosahedral capsids and a long, non-contractile tail. The genomes were double-stranded DNA measuring either 40, 60, 100 or 160 kb. The host range of the phages was examined by infecting 16 bacterial isolates from the floodwater, belonging to Sphingomonas , Novosphingobium , Sphingopyxis and Porphyrobacter . The host range was widely different and varied between infection of only the host used for isolation and infection of hosts belonging to the three genera of Sphingomonas , Novosphingobium and Porphyrobacter . All phages had g23 , indicating the ubiquity of the g23 gene among Myoviridae and Siphoviridae members. Every g23 sequence of the phages belonged to one of the six uncharacterized Paddy Groups proposed by Fujii et al . (2008 ). The g23 sequences were identical at the nucleotide level for several phages with isometric and elongated capsids with 60 and 160 kb genomes, and between some phages and the clones that were retrieved from distant paddy fields. This indicates the common occurrence of horizontal transfer of g23 in the paddy fields. The g23 sequence does not correlate with the host range of those phages. In addition, a larger degree of divergence of g23 from coliphage T4 in paddy fields compared to marine environments was estimated from the present study.     

Myosin substitution rate is affected by the amount of cytosolic myosin in cultured muscle cells

In striated muscles, approximately 300 myosin molecules form a single thick filament in myofibrils. Each myosin is continuously displaced by another myosin to maintain the thick filament structure. Our previous study using a fluorescence recovery after photobleaching (FRAP) technique showed that the myosin replacement rate is decreased by inhibition of protein synthesis, but myosin is still exchangeable. This result prompted us to examine whether myosin in the cytoplasm is involved in myosin replacement in myofibrils. To address this, FRAP was measured in green fluorescent protein (GFP)‐tagged myosin heavy chain 3 (Myh3) expressing myotubes that were treated with streptolysin‐O (SLO), which forms pores specifically in the plasma membrane to induce leakage of cytoplasmic proteins. Our biochemical data demonstrated that the cytoplasmic myosin content was reduced in SLO‐permeabilized semi‐intact myotubes. Furthermore, FRAP experiments showed a sluggish substitution rate of GFP‐Myh3 in SLO‐permeabilized myotubes. Taken together, these results demonstrate that the myosin substitution rate is significantly reduced by a decreased amount of myosin in the cytoplasm and that cytoplasmic myosin contributes to myosin replacement in myofibrils.     

Comparison of bacterial community structures at main habitats in paddy field ecosystem based on DGGE analysis

Bacterial communities at different habitats in a Japanese paddy field ecosystem were compared to understand the bacterial world in the ecosystem as a whole by analyzing data of the denaturing gradient gel electrophoresis (DGGE) band patterns and the sequenced DGGE bands. The habitats were floodwater, percolating water, microcrustacean inhabiting in floodwater, plow layer soil, rice roots, rice straw and rice straw compost incorporated in soil, rice straw placed on the soil surface, plant residues in paddy fields, and rice straw under composting process. Phylotype (band) richness, diversity, evenness, and stability of the bacterial communities at the respective habitats were evaluated based on the DGGE profile data. Phylotype richness was greater near plant residues, rice straw buried in soil and rice straw placed on soil surface, while it was smaller at microcrustacean and rice straw compost buried in soil. The samples from plow layer soil and rice straw compost buried in soil showed considerably higher index values for diversity, evenness, and stability, while those from rice straw placed on soil surface and microcrustacean had lower values of the indices than other habitats. Sequences of totally 250 DGGE bands were assigned to phyla or classes. Distribution of bacterial members to phylogenetic taxa was different among the respective habitats. Inhabitants in plow layer soil were most widely distributed among the groups (nine phyla: Proteobacteria, Chloroflexi, Chlorobi, Verrucomicrobia, Acidobacteria, Nitrospira, candidate division OP10, Cyanobacteria, and Actinobacteria), while those in floodwater and microcrustacean were restricted to only three phyla (Proteobacteria, Bacteroidetes, and Actinobacteria). Proteobacteria and Bacteroidetes were found at all the habitats and the habitats except for plow layer soil, respectively, whereas abundant members belonged to Chloroflexi and Actinobacteria in plow layer soil. “Comprehensive mapping” of DGGE fragments was conducted by principal component analysis based on evolutionary distances of the fragments to 202 reference bacterial strains to overview phylogenetic relationships of bacterial members among the respective habitats. The score plots with the first and second principal components distinctly characterized bacterial members at the respective habitats, and the similarity between the respective communities was clearly demonstrated. Overall, bacterial communities at the respective habitats were distinct and different in the diversity and stability to each other, which may have contributed to the diversity of overall bacterial communities in the paddy field ecosystem.     

Cyanobacterial communities of rice straw left on the soil surface of a paddy field

To estimate diversity, seasonal variation, and phylogeny of the cyanobacterial communities in rice straw placed in nylon mesh bags and left on the soil surface of a paddy field, total DNA was extracted from straw, amplified by polymerase chain reaction targeting 16S rRNA genes of cyanobacteria, and the amplicons were separated by denaturing gradient gel electrophoresis (DGGE). These DGGE bands were sequenced. The paddy field was under flooded condition after transplanting of rice (Experiment 1) and under drained conditions after harvest (Experiment 2). The residual samples on the soil surface under upland conditions were collected just before spring plowing and were placed again on the soil surface after transplanting under flooded conditions. DGGE band patterns of cyanobacterial communities of rice straw were different under drained conditions, under flooded conditions when fresh rice straw samples were placed (Experiment 1), and under flooded conditions when residual rice straw samples were replaced (Experiment 2), indicating that the communities were influenced by both water regime of the paddy field and the degree of the rice straw decomposition. Sequence analysis of DGGE bands indicated that most of the cyanobacteria in rice straw on the soil surface in the paddy field were filamentous members belonging to Subsections III and IV. Filamentous cyanobacterial cells were observed in rice straw under flooded conditions by epifluorescence microscopy.