Bacterial community incorporating carbon derived from plant residue in an anoxic non-rhizosphere soil estimated by DNA-SIP analysis

Purpose

Plant residues are one of the main sources of soil organic matter in paddy fields, and elucidation of the bacterial communities decomposing plant residues was important to understand their function and roles, as the microbial decomposition of plant residues is linked to soil fertility. We conducted a DNA stable isotope probing (SIP) experiment to elucidate the bacterial community assimilating 13-carbon (¹³C) derived from plant residue under an anoxic soil condition. In addition, we compared the bacterial community with that under the oxic soil condition, which was elucidated in our previous study (Lee et al. in Soil Biol Biochem 43:814–822, 2011).

Materials and methods

We used the ¹³C-labeled dried rice callus cells as a model of rice plant residue. A paddy field soil was incubated with unlabeled and ¹³C-labeled callus cells. DNA extracted from the soils was subjected to buoyant density gradient centrifugation to fractionate ¹³C-enriched DNA. Then, polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) analysis of bacterial 16S rDNA band patterns and band sequencing method were used to evaluate bacterial community.

Results and discussion

DGGE analysis showed that the band patterns in the ¹³C-enriched fractions were distinctly changed over time, while the changes in the community structure before fractionation were minor. Sequencing of the ¹³C-labeled DGGE bands revealed that Clostridia were a major group in the bacterial communities incorporating the callus-derived carbon although Gram-negative bacteria, and Actinobacteria also participated in the carbon flow from the callus under the anoxic condition. The proportion of Gram-negative bacteria and Actinobacteria increased on 14 days after the onset of incubation, suggesting that the callus was decomposed by diverse bacterial members on this phase. When the bacterial groups incorporating the ¹³C were compared between under anoxic and oxic soil conditions, the composition was largely different under the two opposite conditions. However, some members of Gram-negative bacteria were commonly found under the anoxic and oxic soil conditions.

Conclusions

The majority of bacterial members assimilating the callus carbon was Clostridia in the soil under anoxic conditions. However, several Gram-negative bacterial members, such as Acidobacteria, Bacteroidetes, and Proteobacteria, also participated in the decomposition of callus under anoxic soil conditions. Our study showed that carbon flow into the diverse bacterial members during the callus decomposition and the distinctiveness of the bacterial communities was formed under the anoxic and oxic soil conditions.

     

The smell and odorous components of dried shiitake mushroom, Lentinula edodes VI: increase in odorous compounds of dried shiitake mushroom cultivated on bed logs

Odor is one of the most important characteristics affecting consumer preference for dried shiitake mushrooms [Lentinula edodes (Berk.) Pegler]. In our previous studies, we found that the odor content of commercial dried products was too weak for most people, and that the odorous compound content could be increased by adding amino acids to sawdust media. Currently, however, bed-log cultivation is used to produce fruiting bodies for dried products. The purpose of this study was to fi nd a method to increase the content of odorous compounds in dried products cultivated on bed logs. Pressure injection of amino acids from the side of the bed log was the most effi cient method, but it had some problems. Hence, a simpler and less troublesome method was developed, i.e., injecting amino acid solution from small bottles set in deep holes bored in the sides of the bed logs. In fruiting bodies cultivated on bed logs injected with amino acid solution by the improved method, the mean contents of lentinic acid, a precursor of the odorous compound lenthionine, approximately doubled compared to that in the untreated logs, although the infi ltration area of the solution injected by the improved method was smaller than that by the former method.     

Comparing the carbon sequestration capacity of temperate deciduous forests between urban and rural landscapes in central Japan

Urbanisation is increasing tremendously in some parts of the world. Consequently, many rural forests may become depleted, although many opportunities exist for urban forests to increase. However, few studies have quantified the carbon (C) sequestration capacities of urban and rural forests in specific climatic zones. The present study compared carbon sequestration in two temperate deciduous forests located in Nagoya and Toyota, central Japan. The Nagoya University forest represented an urban forest, and a site in Toyota represented a rural forest. The urban forest at Nagoya University had comparatively smaller areas of green space and larger areas of buildings and roads. Land uses for building and road, which are typical of urban areas, result in smaller diurnal temperature ranges but higher air temperature, vapour pressure deficit, and atmospheric carbon dioxide (CO₂) concentration. The urban forest in this study exhibited higher gross ecosystem exchange (GEE), especially in the active growing season from May to September, suggesting the possible effect of CO₂ fertilisation. However, higher air temperatures caused comparatively smaller net ecosystem exchange (NEE) because of higher ecosystem respiration (RE). Although both forests functioned as CO₂ sinks at annual time scales, the rural Toyota forest site (5.43 t C ha^–1 yr^–1) had 36% higher net ecosystem production (NEP=–NEE; the negative sign indicates uptake by the forest ecosystem from the atmosphere) than that at the urban forest. The higher normalised respiration (i.e., RE/GPP ratio; GPP=–GEE where GPP represents gross primary production) at the Nagoya University forest might be attributable to factors associated with the degree of urbanisation. Thus, in temperate forests, factors associated with urbanisation may reduce the atmospheric carbon sink function by accelerating respiration. This is an issue of global interest, as many countries are experiencing rapid urbanisation.     

Growth variability of Pacific saury Cololabis saira larvae under contrasting environments across the Kuroshio axis: survival potential of minority versus majority

Growth variability was examined for Pacific saury Cololabis saira larvae under contrasting environments across the Kuroshio axis, based on samples collected during the winter spawning season in 2013 and 2014. The growth rate index (residual of the otolith marginal 3‐day mean increment width from the linear regression on knob length) of larvae was compared among three areas: the inshore side of the Kuroshio axis, the Kuroshio axis, and the offshore side of the Kuroshio axis in relation to sea surface temperature (SST), salinity (SSS) and chlorophyll‐a (CHL) concentration. The larvae were more densely distributed in the Kuroshio axis and offshore areas of higher temperature and salinity and lower chlorophyll‐a concentration than in the inshore areas of lower temperature and salinity and higher chlorophyll‐a concentration. No marked differences in the growth rate index were found among the three areas, even though the larvae in the inshore areas showed slightly higher growth rates in 2013. Despite the broad ranges of environmental factors, no clear relationship between the growth rate index and any environmental factor was detected. The survival potential of Pacific saury larvae was considered to be at least comparable under contrasting environments across the Kuroshio axis. Such a geographical homogeneity is concluded to be attributable to compensable effects of physical and biological factors. We hypothesize that the minority under physically‐unfavorable but biologically‐favorable conditions on the inshore side of the Kuroshio axis could survive equally well as the majority under physically‐favorable but biologically‐unfavorable conditions around the Kuroshio axis and on the offshore side of the Kuroshio axis.     

Relationship between coastal water properties and adult return of chum salmon (Oncorhynchus keta) along the Sanriku coast,Japan

We investigated the relationship between adult (age‐4) return rates for chum salmon (Oncorhynchus keta) originating from the Iwate Prefecture, Japan, and coastal environmental conditions during their early ocean life in coastal residency. We analyzed distributions of water properties via intensive hydrographic observations using a conductivity–temperature–depth profiler. Both the return rates and water properties vary strongly over interannual time scales. We found that the time when the return rate decreased drastically corresponded well to the time when the frequency of warm waters in the coastal residency increased.     

Bacterial community composition of sediments from a milkfish Chanos chanos Forsskål farm

Bacterial communities in sediments underneath milkfish cages and adjacent off‐cage areas in Bolinao, Lingayen Gulf, West Philippine Sea were characterized using PCR‐denaturing gradient gel electrophoresis to assess influence of the fish farming to the sediments. The sediments in the fish cage (FC) area showed anoxic conditions [redox potential of ?165 to ?213 mV and acid‐volatile sulphide‐sulphur (AVS‐S) of 0.55–1.88 mg g^?1 (dry weight)] compared to the relatively oxic off‐cage area [redox potential of 72–81 mV and AVS‐S of 0.09–0.14 mg g^?1 (dry weight)]. The composition of the microbial populations revealed influence of the fish feed sedimentation with higher dominance of putative sulphate‐reducing bacteria (SRB) in the FC area. Compositions of the bacterial taxa showed dominance of the Bacteroidetes group and Deltaproteobacteria. The results suggest that the fish feeds created a new suitable environment, in which reductive microorganisms such as SRB, ferric‐ion‐reducing bacteria and nitrate‐reducing bacteria can thrive. Organic load from the feed and quantity of its leftover constituents may be the key factors that influence the structure of the bacterial community in the sediments of the milkfish farms.     

An avirulence gene homologue in the tomato wilt fungus Fusarium oxysporum f. sp. lycopersici race 1 functions as a virulence gene in the cabbage yellows fungus F. oxysporum f. sp. conglutinans

Six4, a small protein secreted by Fusarium oxysporum f. sp. lycopersici (Fol) in tomato xylem sap during infection, triggers Fol race 1-specific resistance (I) in tomato. SIX4 is regarded as an avirulence gene. Although SIX4 is considered unique to Fol race 1, we detected this gene in the cabbage yellows fungus F. oxysporum f. sp. conglutinans (Foc) by PCR. Because the genes from Foc and SIX4 in Fol were >99 % identical at the nucleotide level, the Foc gene was designated FocSIX4. The expression of FocSIX4 was detected by RT-PCR in stems and roots of cabbage 8 days after infection with Foc. In contrast with Fol, disruption of FocSIX4 in Foc did not increase virulence to Foc-resistant cabbage cvs. Shutoku-SP and Koikaze. On the contrary, the disruptants had reduced virulence not only on Foc-resistant cultivars but also on Foc-susceptible cv. Shikidori. These results suggested that FocSIX4 is involved in virulence, but not in avirulence, in the cabbage yellows fungus.     

First report of black scurf on carrot caused by binucleate Rhizoctonia AG-U

Black scurf on carrot roots was found in Hokkaido, Japan, in 2010. An isolate of a binucleate Rhizoctonia was obtained from sclerotia on the root surface. This isolate was identified as anastomosis group (AG)-U based on cultural characteristics, hyphal fusions and the sequence of ribosomal DNA-internal transcribed spacer region. The AG-U isolate caused black scurf symptoms on carrot roots in an inoculation test. The reference isolate of Rhizoctonia solani AG-2-2 IV, which causes carrot root rot, a disease with symptoms that differ from the black scurf symptom. This is the first report of carrot black scurf caused by binucleate Rhizoctonia AG-U.