Alphaproteobacteria communities depend more on soil types than land managements

Soil properties and agricultural practices take a joint effect on the communities of soil bacteria. The aim of the present study was to survey Alphaproteobacterial communities as possible indicators of soil quality considering clay, loamy and sandy soils under conventional and organic farming. Alphaproteobacteria community composition were analysed by 16S rRNA gene with nested-PCR (polymerase chain reaction) and denaturing gradient gelelectrophoresis (DGGE). Sequencing of partial 16S rRNA gene from the DGGE bands were performed. Conventional and organic farming resulted in significant differences in chemical properties of soils. According to the results community fingerprints were separated into groups depending on soil types and farming systems. This separation can be attributed mostly to soil pH, AL-P₂O₅,-K₂O. The analysed sequences were identified as soil bacteria which could play the main role in nitrogen fixing, mineralisation and denitrification. The highest diversity index was revealed from the organic farming at sandy texture site, where mainly Mesorhizobium sp. and Rhizobium sp. were detected. The soil type and actual crop could have a stronger impact on the soil bacterial composition than the management.     

Vertical Changes in Bacterial Communities in Percolating Water of a Japanese Paddy Field as Revealed by PCR-DGGE

Percolating water was sampled from the plow layer and subsoil layer in a Japanese paddy field, and the bacterial communities were compared together with floodwater by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) targeting a partial 16S rRNA gene and subsequent sequencing. The number of DGGE bands ranged from 16 to 28 with no significant differences among the sampling sites and times. Only 2 bands were common for the three sources of water samples. DGGE bands specific for the floodwater samples and percolating water samples from the plow layer were identified, while percolating water samples from the subsoil layer did not show specific bands but displayed common bands to those of the floodwater samples (7 bands) and percolating water samples from the plow layer (1 band). Cluster analysis of the DGGE banding patterns showed a distinct clustering in the samples of percolating water from the plow layer and a closer relationship between the others. These results suggest that the bacterial communities in percolating water changed during downward movement through the plow layer and subsoil layer. Sequences of the DGGE bands specific for the samples of percolating water from the plow layer showed a close relationship with anaerobic bacteria such as iron-reducers or uncultured bacterial DNA isolated from environments that are considered to be less oxic. On the other hand, the sequences of the bands specific for the samples of floodwater and percolating water from the subsoil layer showed a close relationship with uncultured bacterial DNA isolated from freshwater environments.     

Altitudinal terrestrial isopod diversity

We have assessed the diversity of terrestrial isopods across an elevational and habitat gradient on Mt. Panachaiko (NW Peloponnisos, Greece). Previous knowledge on the biodiversity of this mountain was restricted to very few records of individual species, and no systematic sampling had ever been applied for any animal taxon. We selected the most representative habitat types within an altitudinal range from 750 to 1700 m a.s.l., where we applied qualitative and quantitative monthly sampling using hand collecting and pitfall traps for 6 months during the snow-free period (June–November). We sampled three sites with maquis vegetation, one site with fir forest, one with sparse hawthorn vegetation and two at a highland meadow, and we compared the distribution and abundance patterns of isopod species among these habitat types. Overall, 13 isopod species were found, seven of which were also captured in pitfall traps. One species, Armadillidium lobocurvum, was extremely abundant at the most elevated sites, resulting in very uneven patterns of abundance. The habitat types with higher diversity of isopod species were the sparse hawthorns and the open maquis, and the richest month was July. We also discuss the phenology of the most abundant species at the highland meadows.     

Structural and functional diversity of soil microbes is affected by elevated [CO<Subscript>2</Subscript>] and N addition in a poplar plantation

Background, Aims, and Scope  The genetic structure and the functionality of soil microbes are both important when studying the role of soil in the C cycle in elevated CO₂ scenarios. The aim of this work was to investigate the genetic composition of the fungal community by means of PCR-DGGE and the functional diversity of soil micro-organisms in general with MicroResp-based community level physiological profiling (CLPP) in a poplar plantation (POPFACE) grown under elevated [CO₂] with and without nitrogen fertilization. Materials and Methods  The POPFACE experimental plantation and FACE facility are located in central Italy, Tuscania (VT). Clones of Populus alba, Populus nigra and Populus x euramericana were grown, from 1999 to 2004, in six 314 m² plots treated either with atmospheric (control) or enriched (550 μmol mol⁻¹) CO₂ with FACE (Free Air CO₂ Enrichment) technology in each growing season. Each plot is divided into six triangular sectors, with two sectors per poplar genotype: three species × two nitrogen levels. After removal of the litter layer one soil core per genotype (10 cm wide, 20 cm depth) was taken inside each of the three sectors in each plot, for a total of 36 soil cores (3 replicates × 2 [CO₂] × 2 fertilization × 3 species) in October 2004 and in July 2005. DNA was extracted with a bead beating procedure. 18S rDNA gene fragments were amplified with PCR using fungal primers (FR1 GC and FF390). Analysis of CLPP was performed using the MicroResp method. Carbon substrates were selected depending on their ecological relevance to soil and their solubility in water. In particular rhizospheric C sources (carboxylic acids and carbohydrates) were chosen considering the importance of root inputs for microbial metabolism. Results  The fertilization treatment differentiated the fungal community composition regardless of elevated [CO₂] or the poplar species; moreover the number of fungal species was lower in fertilized soil. The effect of elevated [CO₂] on the fungal community composition was evident only as interaction with the fertilization treatment as, in N-sufficient soils, the elevated [CO₂] selected a different microbial community. For CLPP, the differ ent poplar species were the main factors of variation. The FACE treatment, on average, resulted in lower C utilization rates in un-fertilized soils and higher in fertilized soils. Discussion  Fungal biomass and fungal composition depend on different factors: from previous studies we know that the greater quantity and the higher C/N ratio of organic inputs under elevated [CO₂] influenced positively the fungal biomass both in fertilized and in un-fertilized soil, whereas nitrogen availability resulted to be the main determinant of fungal community composition in this work. Whole active microbial community was directly influenced by the soil nutrient availability and the poplar species. Under elevated CO₂ the competition for N with plants strongly affected the microbial communities, which were not able to benefit from added rhizospheric substrates. Under Nsufficient conditions, the increase of microbial activity due to [CO₂] enrichment was related to a more active microbial community, favoured by the current availability of C and N. Conclusions  Different factors influenced the microbial community at different levels: poplar species and root exudates affected the functional properties of the microbial community, while the fungal specific composition (as seen with DGGE) remained unaffected. On the other hand, factors such as N and C availability had a strong impact on the community functionality and composition. Fungal community structure reflected the availability of N in soils and the effect of elevated [CO₂] on community structure and function was evident only in N-sufficient soils. The simultaneous availability of C and N was therefore the main driving force for microbial structure and function in this plantation. Recommendations and Perspectives  Using the soil instead of soil extracts for CLPP determination provides a direct measurement of substrate catabolism by microbial communities and reflects activity rather than growth because more immediate responses to substrates are measured. Further applications of this approach could include selective inhibition of different microbial functional groups to investigate specific CLPPs. To combine the structural analysis and the catabolic responses of specific microbial communities (i.e. fungi or bacteria) could provide new outlooks on the role of microbes on SOM decomposition. ESS-Submission Editor: Dr. Kirk Semple (k.semple@lancaster.ac.uk)     

Response of microbial communities to water stress in irrigated and drought-prone tallgrass prairie soils

To better understand how water stress and availability affect the structure of microbial communities in soil, I measured the change in phospholipid fatty acids (PLFA) and the incorporation of ¹³C-labeled glucose into the PLFA following exposure to water stress. Overlaid on the laboratory water stress treatment, samples were collected from drought-prone and irrigated (11 years) tallgrass prairie soil (0-10 cm depth). In the laboratory, soils were either incubated at −250 kPa or dried steadily over a 3-d period to −45 MPa. On the fourth day, the dried samples were brought up to −250 kPa and then all samples received 250 μg of glucose-C (+4000 δ¹³C-PDB) solution that brought them to −33 kPa matric water potential. Samples were then extracted for PLFA following 6 and 24 h of incubation (25 °C). Non-metric multidimensional scaling (NMS) techniques and multi-response permutation procedure (MRPP) showed that the largest effect on the mol% distribution of PLFA was related to the field scale water addition experiment. In response to irrigation, the PLFA 16:1ω5, 18:1+, and 18:2ω6,9 showed increases, and a15:0, a17:0, and cy19:0 showed decreases in their respective mol%. Effects related to the induction of laboratory water stress were predominantly associated with a decrease in the mol% distribution of the putative fungal biomarker (18:2ω6,9) with little to no change in the mol% distribution of the bacterial biomarkers. Interestingly, the flow of C to the microbial community was not strongly related to any single PLFA, and differences were rather subtle, but multivariate MRPP detected change to the community structure related to the laboratory water stress treatment but not related to the 11 years of field irrigation. Our results suggest that both the total and the actively metabolizing bacterial community in soil were generally resistant to the effects of water stress brought by rewetting of dry soil. However, more research is needed to understand the nature of the fungal response to drying and rewetting in soil.     

Analysis of bacterial communities in soil by PCR-DGGE targeting protease genes

We studied the effects of the application of organic (OM) and inorganic fertilizer (CF) on soil protease activity and proteolytic bacterial communities in rhizosphere and bulk soil on an experimental lettuce field in Hokkaido, Japan. The protease activity always was higher in soils of the OM than with the CF treatment, and also higher in the rhizosphere than in the bulk soil. We analyzed proteolytic bacterial communities by denaturing gradient gel electrophoresis (DGGE) of the alkaline metalloprotease (apr) and neutral metalloprotease (npr) genes. Most apr forms detected were closely related to apr of Pseudomonas fluorescens, and all npr variants closely resembled the gene of Bacillus megaterium. These results were consistent with findings from tests using cultured bacterial communities, indicating a high specificity of our PCR-DGGE for amplifying apr and npr genes. The community compositions of proteolytic bacteria were assessed by principal component analysis of the DGGE profiles. There were significant differences in the effects of CF and OM on the community compositions of apr- and npr-expressing bacteria, and the communities of the two types of bacteria played different roles in rhizosphere and bulk soil. We found significant correlations between the protease activity and the communities of the two types of bacteria. The results indicate that different proteolytic bacteria release different amounts or activities of protease, and that the composition of proteolytic bacterial communities may play a major role in determining overall soil protease activity.     

Impact of heavy metals on the degradative capabilities of soil bacterial communities

The degradative capabilities of six heavy-metal-affected and six unaffected bacterial communities from Canadian and German soils were determined by enumerating colony-forming units on 20 specific media. Each of these contained an aromatic substrate as the sole source of C and energy. Comparisons of plate counts revealed that heavy metal stress caused a decrease in the eveness of the distribution of the 20 degradative capabilities This suggests that in heavy-metal-affected bacterial communities, relatively rare degradative capabilities, irrespective of their nature, are even rarer than in unaffected communities, while the reverse is true for more common capabilities. The results are discussed with respect to the ease with which aromatic substrates can serve as C and energy sources.     

滇中三种人工林群落控制土壤侵蚀和改良土壤效应

通过对人工云南松群落、桉树—黑荆混交林群落、直干桉群落及无林地对照地表径流、土壤侵蚀的观测及林地土壤几个主要理化指标的分析表明 ,地带性植物种云南松形成的人工林群落及桉—黑荆混交林具有好的控制径流和土壤侵蚀的能力 ,对土壤理化性质的改善也有较明显的作用 ,值得在生产中推广。在此基础上 ,论述了不同人工林群落土壤理化性质的改善与土壤侵蚀的控制关系。     

密云水库上游北庄试验区植被性质的初步研究

通过对植物区系和植物群落的调查分析，研究了北京低山区密云水库上游北庄试验区的植被性质，以为本区的造林经营提供理论依据     

哈尔滨市不同绿地植物群落重金属分析与种植对策

采用野外调查与室内实验分析相结合的方法,以哈尔滨市街道广场绿地、单位附属绿地、苗圃生产绿地的“乔灌草密林、乔灌草疏林、灌木密林”植物群落为研究对象,综合评价不同植物群落土壤的重金属Zn、Cu、Pb含量与污染程度,对比分析不同植物群落的重金属修复效应及树木含水量、全氮、全磷含量与土壤重金属富集的相关性.结果表明:土壤重金属修复能力为乔灌草密林＞灌木密林＞乔灌草疏林;植物根系重金属富集能力最强,其中小根对锌、铜富集能力较强,大根、中根对铅富集能力较强;树种富集重金属能力显著不同,梓树、黄檗对铜富集能力较强,铺地柏、红皮云杉、小叶丁香对铅富集能力较强,紫丁香、胡桃楸对锌富集能力较强;树木富集铜和锌的能力与其叶片含水量、叶片全磷含量密切相关.为了有效修复土壤重金属污染,提出了优先选用耐重金属植物、努力提高乔灌木小根数量、科学营造乔灌草复层群落等种植对策.