The capacious hologenome

Blending disciplines can be transformative in science, yet interdisciplinary mergers should not escape healthy skepticism. Indeed, the history of biology shows us that debates about the relative importance of nuclear genetics vs. microbial symbiosis in eukaryotic biology are among the most engaging. Today's technology may help resolve this century old debate as it illuminates the interwoven genomics and functions of symbionts with their host genome. Thus, we can now assert that all subdisciplines of zoology require microbiology. Although controversial to some, the evidence from studies of host-associated microbial communities indicates that metazoans are hologenomes – interconnected compositions of animal and microbes.     

Solid-phase distribution of heavy metals as affected by single reagent extraction in dredged sediment derived surface soils

ABSTRACT

EDTA is useful to assess mobile metal pools in polluted soils and sediments. There is a need to enhance our understanding of the significance of metal fractions released. The impact of single reagent extraction with 0.05 mol L^?1 EDTA on the solid phase distribution of trace metals in surface soils sampled from confined dredged sediment disposal sites was investigated. Not extracted and EDTA extracted soils were subjected to sequential extraction to fractionate the total contents into: (1) easily exchangeable and carbonate bound fraction; (2) reducible fraction; (3) oxidisable fraction; and (4) residual fraction. With EDTA, significant portions of metals associated with the acid extractable and reducible fractions were released. The oxidisable and residual fractions remained unaffected for most of the investigated metals except for the organic matter associated metals (Cu and Pb). A decrease in the residual fraction after EDTA-extraction for Cu and Pb was attributed to artifacts of the sequential extraction procedure.     

Coexistence of two congeneric tree species of Lauraceae in a secondary warm‐temperate forest on Miyajima Island,south‐western Japan

We analyzed the spatial distributions of two congeneric tree species, Neolistea aciculata and Neolistea sericea (Lauraceae), in a warm‐temperate forest on Miyajima Island, south‐western Japan. Both species were mainly found in valley sites on the island. Hence, these species shared the same topographic habitat niche. However, we found a clear difference between the spatial distributions of the two species in relation to the light environment. Neolistea aciculata was predominantly found in stands with low light, such as beneath the canopy of dense evergreen broadleaved forest. In contrast, N. sericea was predominantly associated with ample light, such as in secondary Pinus densiflora forest. In stands with moderate light conditions, both species were found. This habitat niche segregation in relation to light conditions presumably allows the coexistence of these two species in the predominantly successional forest on Miyajima Island.     

Flow cytometric assessment of cytotype distributions within local populations of Phragmites australis (Poaceae) around Lake Biwa,the largest lake in Japan

Phragmites australis (Poaceae) is a clonal perennial that is an important component of wetland ecosystems worldwide. Using flow cytometry, we examined the cytotype distributions within five populations of P. australis located in the vicinity of Lake Biwa. As in previous reports, two ploidy levels, octoploid (2n = 8x = 96) and decaploid (2n = 10x = 120), were identified, which are assumed to be the main cytotypes around the lake. The coexistence of two cytotypes was detected in four of the five populations, suggesting the relatively common occurrence of mixed ploidy levels in the populations around Lake Biwa. Although intermingled cytotype distributions were observed in some populations, the 9x cytotype, that is, the expected outcome of inter‐cytotype crosses, was not observed, indicating limited gene flow between the two cytotypes.     

Multiple Induction of Dye-Linked Aromatic Alcohol Dehydrogenases by n-Propanol and rc-Butanol in Rhodopseudomonas acidophila M402

We visualized flavonol distribution in the abaxial epidermis of onion scales without chemical processes via detection of blue-light-induced green autofluorescence. Our visualizing results indicated an unequal intercellular distribution of flavonols among epidermal cells causing a patch distribution in the epidermis, and indicated that flavonol accumulation in ultraviolet irradiated-onion scales was in uniformity with epidermal cells, probably to compensate for their stress-hypersensitiveness.     

Incorporation of Glycine and Serine into Sporulating Cells of Bacillus subtilis

The changes during growth and sporulation in activities of cells of Bacillus subtilis to incorporate various amino acids were investigated with wild-type strain and its asporogenous mutant. In the case of wild type strain the uptake of valine, phenylalanine, and proline was largest during the logarithmic growth period. The uptake of these amino acids decreased rapidly during the early stationary phase. The uptake of valine and cysteine increased again to some extent just prior to the forespore stage. The uptake of glycine and serine, however, was largest at the forespore stage at which the formation of spore coat took place. From these observed phenomena it was assumed that the remarkable incorporation of glycine and serine into the wild type strain during sporulation was closely related to the formation of spore coat.     

Guanosine Diphosphate Mannose in Conformational Relation to Other Suger Nucleotides and Phosphates in Solution

Molecular conformational transition of GDPMan and solution conformation of α-d- mannopyranose moiety in Man-l-P and GDPMan were examined in relation to other sugar nucleotides and phosphates. GDPMan and other sugar nucleotides examined revealed changes in the optical rotation in sigmoidal curve in water by addition of urea. The change was reversible without significant decomposition and is attributable to dissociation of an ordered form into a random form. Optical conformational values in 8m urea solution were+116° for GDPMan, +58°~+79° for UDPGlc, +79° for UDPGal, +135°~+143° for UDPGlcNAc, and +138°~ +155° for UDPGIcA.

NMR analysis and periodate oxidation study revealed the ⁴C₁ conformation of α-d-hexopyranose moieties in Man-1-P, Glc-l-P, GDPMan, UDPGlcNAc and UDPGalNAc.     

Effects of Exogenous Zinc on the Cellular Zinc Distribution and Cell Cycle of A549 Cells

Carotenogenesis in Nocardioform actinomycete Rhodococcus rhodochrous was investigated using carotenogenesis mutants and inhibitors, and a postulated carotenogenesis pathway was proposed. At the end of the synthesis, fatty acid or mycolic acid was esterified by different esterases to the same C-6 hydroxyl group of β-D-glucoside.     

Histochemical Studies of the Non‐Host Resistance and the Role of Actin Cytoskeleton in Pepper Against Colletotrichum orbiculare

The penetration process and defence reactions (hypersensitive response, oxidative burst and cell wall fortification) of Colletotrichum orbiculare were studied histochemically on pepper cultivar ‘A11’ (non‐host) and susceptible cucumber cultivar ‘Changchun Thorn’ (host). The results indicate that C. orbiculare could hardly penetrate the non‐host pepper leaves. It was papillae rather than hypersensitive response and H₂O₂ that played an important role in resisting the colonization and development of C. orbiculare on the non‐host pepper. The depolymerization of the actin microfilament weakened the papilla deposition of pepper and allowed successful penetration of the non‐adapted C. orbiculare, suggesting that the actin cytoskeleton of pepper is significant in preventing the invasion of the non‐host pathogen C. orbiculare.     

Taxonomic Characterization and Experimental Host Ranges of Four Newly Recorded Species of Alternaria from Japan

Alternaria fungi are important plant pathogens. Here, we identified three species new to the Japanese mycoflora: Alternaria celosiae, Alternaria crassa and Alternaria petroselini. We proposed a new name for A. celosiae (E.G. Simmons & Holcomb) Lawrence, Park & Pryor, a later homonym of A. celosiae (Tassi) O. S?vul. To characterize these and a fourth morphological taxon, Alternaria alstroemeriae, which was recently added to Japan's mycoflora, an integrated species concept was tested. We determined the host range of each isolate using inoculation tests and analysed its phylogenetic position using sequences of the internal transcribed spacer rDNA. The pathogenicity of our A. alstroemeriae isolate was strictly limited to Alstroemeria sp. (Alstroemeriaceae), but the species was phylogenetically indistinguishable from other small‐spored Alternaria. Alternaria celosiae on Celosia argentea var. plumosa (Amaranthaceae) was also pathogenic to Amaranthus tricolor, to Alternanthera paronychioides and weakly to Gomphrena globosa (all Amaranthaceae) and formed a clade with the former Nimbya celosiae. Alternaria crassa on Datura stramonium (Solanaceae) was also pathogenic to Brugmansia × candida and Capsicum annuum in Solanaceae, but not to other confamilial plants; phylogenetically it belonged to a clade of large‐spored species with filamentous beaks. Morphological similarity, phylogenetic relationship and experimental host range suggested that A. crassa, Alternaria capsici and Alternaria daturicola were conspecific. Alternaria petroselini on Petroselinum crispum (Apiaceae) was pathogenic to five species in the tribe Apieae as well as representatives of Bupleureae, Coriandreae, Seliaeae and Scandiceae in Apiaceae. Both phylogeny and morphology suggested conspecificity between A. petroselini and Alternaria selini.