Bacterial and fungal community composition and community-level physiological profiles in forest soils.

We characterized the potential functioning and composition of the bacterial and fungal communities in the O and A horizons of forest soils using community-level physiological profile (CLPP) based on BIOLOG analysis, and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis of 16S and 18S rDNA fragments, respectively. In addition, relationships between the potential functioning and the community composition in each horizon, and between the O and A horizons, were assessed using Procrustes analysis. For the bacterial and fungal communities, the CLPP and DGGE profile were clearly separated between the O and A horizons in a principal coordinate analysis except for the fungal CLPP. No significant links for CLPP and DGGE profile between the O and A horizons were observed for either bacterial or fungal communities, suggesting that different factors had considerable influence on the microbial communities between the O and A horizons. Significant couplings between bacterial and fungal DGGE profiles (p <0.05 for O horizon; p <0.01 for A horizon), and between bacterial and fungal CLPPs (p = 0.001 for O horizon; p <0.01 for A horizon), were observed in the O and A horizons, implying that common factors strongly influenced the bacterial and fungal communities in each horizon. Although a significant correlation was observed between bacterial community composition and the potential functioning in the A horizon (p <0.01), such a correlation was not observed for the fungal community in the A horizon, and for the bacterial and fungal communities in the O horizon. This finding suggested that potential functioning, which would reflect only rapidly growing microorganisms, was not strongly associated with the composition of the entire microbial community. Further studies are needed to unravel the factors shaping the composition and functioning of microbial communities in forest soils

Identification of the gene for disaggregatase from Methanosarcina mazei

The gene sequences encoding disaggregatase (Dag), the enzyme responsible for dispersion of cell aggregates of Methanosarcina mazei to single cells, were determined for three strains of M. mazei (S-6T, LYC and TMA). The dag genes of the three strains were 3234 bp in length and had almost the same sequences with 97% amino acid sequence identities. Dag was predicted to comprise 1077 amino acid residues and to have a molecular mass of 120 kDa containing three repeats of the DNRLRE domain in the C terminus, which is specific to the genus Methanosarcina and may be responsible for structural organization and cell wall function. Recombinant Dag was overexpressed in Escherichia coli and preparations of the expressed protein exhibited enzymatic activity. The RT-PCR analysis showed that dag was transcribed to mRNA in M. mazei LYC and indicated that the gene was expressed in vivo. This is the first time the gene involved in the morphological change of Methanosarcina spp. from aggregate to single cells has been identified

Nitrogen supply rate regulates microbial resource allocation for synthesis of nitrogen-acquiring enzymes.

Although microorganisms will preferentially allocate resources to synthesis of nitrogen (N)-acquiring enzymes when soil N availability is low according to the resource allocation model for extracellular enzyme synthesis, a robust link between microbial N-acquiring enzyme activity and soil N concentration has not been reported. To verify this link, we measured several indices of soil N availability and enzyme activity of four N-acquiring enzymes [N-acetyl-β-glucosaminidase (NAG), protease (PR), urease (UR), and L-asparaginase (LA)] and a carbon (C)-acquiring enzyme [β-D-glucosidase (BG)] in arable and forest soils. Although the ratios of NAG/BG and PR/BG were not significantly related with indices of soil N availability, ratios of LA/BG and UR/BG were strongly and negatively related with potentially mineralizable N estimated by aerobic incubation but not with pools of labile inorganic N and organic N. These results suggest that microorganisms might allocate their resources to LA and UR synthesis in response to N supply rate rather than the size of the easily available N pools. It was also suggested that the underlying mechanism for synthesis was different between these N-acquiring enzymes in soil microorganisms: microbial LA and UR were primarily synthesized to acquire N, whereas NAG and PR syntheses were regulated not only by N availability but also by other factors

Predicting arbuscular mycorrhizal fungal colonization of soybean in farmers’ fields by using infection unit density

Estimating arbuscular mycorrhizal (AM) fungal activity to colonize crop root before cultivation is prerequisite for effective utilization of their functions which enhance growth and yield of the plant especially under low fertilizer input. We have hypothesized that the infection unit (IU) density formed on test plant roots grown for short period (12 days) with soil sampled from soybean production fields would be an effective indicator to predict AM fungal colonization intensity to the plant. In order to test this hypothesis, three-year farmland survey was conducted, in which soil samples before sowing soybean and the plant root samples at third trifoliate (V3) and full bloom (R2) stage were collected from farmers’ fields in two regions in Hokkaido, Iwamizawa and Tokachi. For each sampling spot, IU density was determined by using test plants, and intensity of AM fungal colonization of soybean root was measured. Before pursuing field survey, laboratory experiments were conducted to find out proper soil storage condition that keeps IU density unchanged while handling many soil samples. Our results indicated that IU density was almost comparable to the original value after six-month storage if soil samples were kept in a refrigerator, although storing at ambient temperature significantly decreased the measurement. Air drying also had negative impact on IU density. According to the field survey, IU densities determined using field soil were positively and significantly correlated with AM fungal colonization of soybean roots at both V3 and R2 stages. Differences in climate, soil type, and style of agriculture between Iwamizawa and Tokachi seemed to have little effect on IU density-AM fungal colonization relationship. Other than IU density, soil pH and soil penetration resistance at 10 cm depth were selected as significant explanatory variables for predicting AM fungal colonization by multiple regression analysis. However, IU density was the most influential factor among three. Therefore, IU density is recognized as an effective measure to evaluate AM fungal colonizing activity in field soil.</p