The bacterial diversity in surface sediment from the South China Sea

16S rDNA sequencing results from this study and literatures demonstrate that sediment bacteria in the South China Sea （SCS） were very diverse,which contained 22 of the 24 phyla of bacteria investigated from marine sediment,however,it was very imbalance among stations.So bacterial diversity from 15 samples which covered a wide range of sediment types from 20 to 3 888 m in depth was studied in DGGE （denature gradient gel electrophoresis） in this paper.The DGGE results indicate that both sediment bacterial diversity and diversity difference among stations were significant.Thirty representative and differential fingerprints among samples were recovered and sequenced,phylogenetic analysis indicates that they may belong to Proteobacteria （α-,β-,γ-,δ-,ε-）,Planctomycetes,Firmicutes,Chloroflexi,Acidobacteria,Actinobacteria,Nitrospirae,Gemmatimonadetes,candidate division WS3 and so on,of which,Gemmatimonadetes and candidate division WS3 bacteria were first detected in SCS sediment.This study also shows that bacterial diversity analysis based on DGGE was more potential than traditional 16S rDNA clone library in multiple sample analysis.

Bacterial diversity in activated sludge from a consecutively aerated submerged membrane bioreactor treating domestic wastewater

The bacterial diversity of activated sludge from submerged membrane bioreactor (SMBR) was investigated. A 16S rDNA clone library was generated, and 150 clones were screened using restriction fragment length polymorphism (RFLP). Of the screened clones, almost full-length 16S rDNA sequences of 64 clones were sequenced. Phylogenetic tree was constructed with a database containing clone sequences from this study and bacterial rDNA sequences from NCBI for identification purposes. The 90.6% of the clones were a?l...

The bacterial diversity and community composition altered in the oxygen minimum zone of the Tropical Western Pacific Ocean

The oxygen minimum zones(OMZs)are globally expanding,yet the variation pattern of microbial communities related to dissolved oxygen levels remain unclear.Spatial variability of bacterial diversity and community composition(repre sented by 16 S rRNA)of six stations was investigated within the water column in the seamount area of Tropical Western Pacific Ocean(TWPO)in May 2019.The seawater has dissolved oxygen(DO)concentration of 3.01-6.68 mg/L and the core of the oxygen minimum zones was located between the depths of 650 m and 1750 m.The bacterial alpha-diversity showed unimodal pattern with the decreasing DO with depths and peaked in the upper oxycline(UO)of OMZs.The bacterial community structure of the mixed layer(ML)and the bottom layer clustered and separated from each other,while those of UO and the OMZ core(OM)clustered and overlapped.Overall,bacterial community composition transitioned from being Alphaproteobacteria and Gammaproteobacteria-dominant in ML to being Gammaproteobacteria and Nitrososphaeria/Deltaproteobacteria-dominant in UO and OM,and then changed to being Clostridia and unidentified Actinobacteria-dominant in the bottom layer.Moreover,both bacterial alpha-diversity and the abundant classes fitted varying sectioned functions with DO.The DO solely explained 40.37%of the variation of bacterial community composition among layers(P<0.001).The predicted function profiling showed that the water column was predominant by chemoheterotrophy,cyanobacteria,and photoautotrophy in ML,by chemoheterotrophy and nitrate/sulfide cycling in UO and OM,and by chemoheterotrophy and ferme ntation in the bottom layer.Our findings revealed the DO-associated variation in bacterial diversity and community composition,and help to clarify the potential responses of microbes and their involved biogeochemical processes to the expansion and intensification of OMZs.

Bacterial diversity in the sediment of Crescent Moon Spring,Kumtag Desert,Northwest China

Desert lake, a unique oasis in desert ecosystems, harbours different bacterial communities. Thus, it is considered as a hub of bacterial diversity. In this study, bacterial diversity in the sediment of Crescent Moon Spring, Kumtag Desert, Northwest China was analyzed using high-throughput amplicon pyrosequencing analysis. The sequences of the most abundant OUTs （Operational Taxonomic Units） in the sediment of Crescent Moon Spring were compared with the sequences of those most abundant OUTs of various origins from NCBI GenBank database to detect the origins of bacteria in the sediment of Crescent Moon Spring. Also, bacterial compositions between sediment of Crescent Moon Spring and other desert and lake ecosystems （including desert lakes） worldwide were compared using cluster analysis to determine the possible factors affecting bacterial compositions. In total, 11,855 sequences were obtained and 30 phyla were identified. At the phylum level, the dominant phylum was Proteobacteria with α-Proteobacteria being the first dominant class and the second dominant phylum was Planctomycetes. Our finding that α-Proteobacteria being the first dominant class of Proteobacteria and Planctomycetes being the second dominant phyla are somewhat contradictory with reports from other desert lake sediments. This difference could be resulted from water hydration and conductivity, as well as oligotrophic conditions of Crescent Moon Spring. At the genus level, Rhodobacter, Caldilinea, Planctomyces, and Porphyrobacterwere the dominant genera in the sediment of Crescent Moon Spring. Comparisons on sequences of the most abundant OUTs （including OTU3615, OTU6535, and OTU6646） between sediment of Crescent Moon Spring and various origins from NCBI GenBank database indicate that the origins of bacteria in the sediment of Crescent Moon Spring are likely from the underground water. Furthermore, cluster analysis on comparisons of bacteria compositions between sediment of Crescent Moon Spring and other desert and lake ecosystems （including desert lakes） worldwide shows that at regional scales, bacterial compositions may be mainly affected by geographical patterns, precipitation amounts, and pH values. Collectively, our results provide new knowledge on the bacterial diversity in desert lake ecosystems.

Effects of Continuous Plastic Film Mulching on Soil Bacterial Diversity, Organic Matter and Rice Water Use Efficiency

Two field experiments were conducted to study the effects of 6-year plastic film mulching on bacterial diversity, organic matter of paddy soil and water use efficiency on different soils with great environmental variabilities in Zhejiang Province, China, under non-flooding condition. The experiment started in 2001 at two sites with one rice crop annually. Three treatments included plastic film mulching with no flooding (PM), no plastic film mulching and no flooding (UM), and traditional flooding management (TF). Soil samples were collected and analyzed for bacterial diversity by DGGE and organic matter content, and water use efficiency (WUE) was calculated. The results showed that PM treatment favored the development of a more total bacterial community compared with TF management, the total number of bands was 33.3, 31.7 at tiller stage and heading stage (p < 0.05*). Hence, organic matter content was decreased by 36.7% and 51.4% under PM at two sites. PM also produced similar rice grain yield as TF at Duntou site and Dingqiao site, the average was 7924 kg?ha?1 and 7015 kg?ha?1 for PM and 8150 kg?ha?1 and 6990 kg?ha?1 for TF, respectively. Compared to TF, WUE and irrigation water use efficiency were increased significantly by 70.2% - 80.4% and 273.7% - 1300.0% for PM. It is essential to develop the water-saving agriculture.

Different Decaying Wood Effects on Bacterial Diversity:Insights from Molecular Methods

Decaying wood is a novel key factor required for biodiversity and function of a forest,as it provides a good account of substrate and habitats for various organisms.Herein,the bacterial diversity in decaying wood of Betula platyphylla was discussed through high throughput sequencing.Our results showed that most of the obtained sequences belonged to the phyla Firmicutes,Proteobacteria,Bacteroidetes,Actinobacteria,Acidobacteria and Verrucomicrobia.Bacterial community compositions in samples with higher moisture content were obviously different than that with lower content,which could be reflected by richness estimators,diversity indices,and cluster and heatmap analysis.All three networks were non-random and possessed topological features of complex systems such as small-world and modularity features.However,these networks exhibited distinct topological features,indicating the potential ability of extensive cooperative and competitive interactions in the decayed wood microenvironments.Redundant analysis showed that most bacterial phyla were mainly distributed in highermoisture trunks.The obtained data will increase the knowledge of the complex bacterial diversity associated with dead wood,and lay a foundation for the bioconversion technology of plant cell walls using bacteria.

Bacterial diversity in Arctic marine sediment determined by culture-dependent and-independent approaches

Bacterial diversity in surface sediment from the Arctic Ocean was investigated by culture-dependent and-independent approaches. Conventional culture-dependent techniques revealed 11 strains based on their distinct morphological characteristics on marine Zobell 2216E agar plates. Phylogenetic analysis showed that these isolates belonged to three major lineages of the Bacteria,γ-proteobacteria, Bacteroidetes and Actinobacteria, and that they included 10 genera. Most isolates were psychrotrophic, and NaCl was not necessary for their growth. Furthermore, they exhibited activity of at least one extracellular hydrolytic enzyme at 4＆#176;C and had various abilities to assimilate carbon sources. A total of 67 phylotypes were detected among 142 clones based on the 16S rRNA library of the total community DNA and grouped into nine major lineages of bacteria. Phylotypes afifliated withγ-,δ-andε-proteobacteria accounted for 36.7%, 21.8%and 16.9%of the total clones, respectively. The rest of the clones belonged to Bacteroidetes,α-proteobacteria, Actinobacteria, Fusobacteria, Nitrospirae and an unclassiifed group.

Bacterial diversity in sediments of core MD05-2902 from the Xisha Trough,the South China Sea

A sediment core MD05-2902 was collected from the deep-sea basin of the Xisha Trough. The vertical distribution and diversity of bacteria in the core was investigated through ten sub-sampling with an interval of 1 m using bacterial 16 S rRNA gene as a phylogenetic bio-marker. Eighteen phylogenetic groups were identified from 16 S rRNA gene clone libraries. The dominant bacterial groups were JS1, Planctomycetes and Chloroflexi, which accounted for 30.6%, 16.6%, and 15.6% of bacterial clones in the libraries, respectively. In order to reveal the relationship between biotic and abiotic data, a nonmetric multidimensional scaling analysis was performed. The result revealed that the δ15N, δ13C, total organic carbon and total organic nitrogen possibly influenced the bacterial community structure. This study expanded our knowledge of the biogeochemical cycling in the Xisha Trough sediment.

Effect of long-term continuous cropping of strawberry on soil bacterial community structure and diversity

Long-term monoculture leads to continuous cropping （CC） problems, which complicate agricultural production, both locally and abroad. This study contrasted the different bacterial community compositions, physicochemical properties and enzyme activities of strawberry soil subjected to CC, CC rhizosphere （CCR）, non-CC （NCC） and non-CC rhizosphere （NCCR） treatments. The soil physicochemical properties and enzyme activities were significantly reduced after long-term CC. In addition, five variation trends were observed for the 11 major bacterial genera in the soil. Sphingomonas was the only stable group among all treatments. The proportions of Novosphingobium, Rhodoplanes, Povalibacter, Cellvibrio and Stenotrophobacterdecreased after CC. The relative abundances of Pelagibius, Thioprofundum and AIIokutzneria increased only in the CC treatment. Nitrospira were more abundant in rhizosphere soil than in non-rhizosphere soil. The relative abundance of Bacillus increased after CC. Redundancy analysis revealed that Bacillus, Pelagibius and AIIokutzneria had significant negative correlations with the soil physicochemical properties and enzyme activities. Therefore, these genera may be the key bacteria influenced by the physicochemical properties and enzyme activities altered by replanting. These results indicate that long-term CC of strawberry leads to less favourable rhizosphere soil conditions, which can be understood as a stress-induced response of the bacterial community diversity. Further research is needed to determine how the quality of soil is reduced by the shift in the diversity of the soil bacterial community.

Climate and salinity drive soil bacterial richness and diversity in sandy grasslands in China

Bacteria constitute a large proportion of the biodiversity in soils and control many important processes in terrestrial ecosystems.However,our understanding of the interactions between soil bacteria and environmental factors remains limited,especially in sensitive and fragile ecosystems.In this study,geographic patterns of bacterial diversity across four sandy grasslands along a 1,600 km north-south transect in northern China were characterized by high-throughput 16S rRNA gene sequencing.Then,we analyzed the driving factors behind the patterns in bacterial diversity.The results show that of the 21 phyla detected,the most abundant were Proteobacteria,Actinobacteria,Acidobacteria and Fir‐micutes(average relative abundance>5%).Soil bacterial operational taxonomic unit(OTU)numbers(richness)and Faith's phylogenetic diversity(diversity)were highest in the Otindag Sandy Land and lowest in the Mu Us Sandy Land.Soil electrical conductivity(EC)was the most influential factor driving bacterial richness and diversity.The bacterial communities differed significantly among the four sandy grasslands,and the bacterial community structure was signifi‐cantly affected by environmental factors and geographic distance.Of the environmental variables examined,climatic factors(mean annual temperature and precipitation)and edaphic properties(pH and EC)explained the highest propor‐tion of the variation in bacterial community structure.Biotic factors such as plant species richness and aboveground bio‐mass exhibited weak but significant associations with bacterial richness and diversity.Our findings revealed the impor‐tant role of climate and salinity factors in controlling bacterial richness and diversity;understanding these roles is critical for predicting the impacts of climate change and promoting sustainable management strategies for ecosystem services in these sandy lands.

Bacterial community diversity of meltwater runoff and soil in Midre Lovénbreen glacier in Ny-Alesund,Arctic

Glacial meltwater runoff is a dynamic ecosystem.On the one hand,nutrient concentration changes as it flows from upstream to downstream,and on the other hand,bacterial community structure changes due to its contact with nearby soil during the flow process.We studied meltwater and soil in the Midre Lovénbreen glacier region,to explore changes in bacterial diversity as meltwater flows,and the relationship between meltwater and soil bacterial diversity.As glacial meltwater flows from upstream to downstream,the relative abundance of dominant bacterial groups changes.In addition,we found that during the flowing process,nutrient exchange and bacterial contact had occurred between the meltwater runoff and the soil.As a result,the distribution patterns of some bacteria in the meltwater are very similar to those in the soil.Finally,we combined distance-based redundancy analysis and weighted correlation network analysis to show that NO_(3)^(-)-N and NO_(2)^(-)-N are the most two significant factors affecting glacial meltwater and soil,respectively.Our results suggest that in such a close-knit ecosystem,the interaction of glacial meltwater with soil,as well as environmental factors,together determine bacterial community composition.

Microbiome Diversity Analysis of the Bacterial Community in Idah River, Kogi State, Nigeria

The analysis of bacterial diversity in aquatic systems particularly in rivers, lakes, and streams can provide useful data on the effect of anthropogenic activities on such water bodies to humans and fishes. Idah River, the focal point of this study, is an offshoot of the two major Nigerian rivers characterized by observed human activities and pollution sources. Water samples were collected from four designated sites and assessed for their bacterial assemblages and structure, using PacBio Single-Molecule Real-Time (SMRT) sequencing technology. The full length of the 16S rRNA gene was sequenced, and Amplicon Sequence Variants were generated using the DADA2 workflow optimised for PacBio long-read amplicons in Rstudio. A total of 8751 high-quality reads obtained were taxonomically classified as 24 phyla, 42 classes, 84 orders, 125 families, 156 genera, and 106 species. Taxonomical composition revealed Proteobacteria as the most abundant phyla across all sample sites. At the genera level, Azospira (57.03%) was the most dominant ASV in Docking Point A, while Acinetobacter (66.67%) was the most abundant ASV in Docking Point B. In Idah Axis Confluence, hgcl clade (65.66%) was the most prevalent ASV, whereas Holophaga (42.86%) was the most common ASV in Idah Axis Midstream. Genera analysis also revealed that 12.9% of the total ASVs were discovered across all sample sites. Among these were pathogenic bacteria, reducers, and degraders of domestic and animal wastes. Observed results provide evidence that sampled sites of Idah River are contaminated, most likely through constant human activities and thus, could have an impact on resident fishes as well. This study, therefore, agrees with a previous report from the river, which used standard microbial procedures. However, next-generation sequencing techniques employed revealed more bacterial community than the former, including unresolved taxonomic sequences that may be novel.

Plant property regulates soil bacterial community structure under altered precipitation regimes in a semi-arid desert grassland, China

Variations of precipitation have great impacts on soil carbon cycle and decomposition of soil organic matter.Soil bacteria are crucial participants in regulating these ecological processes and vulnerable to altered precipitation.Studying the impacts of altered precipitation on soil bacterial community structure can provide a novel insight into the potential impacts of altered precipitation on soil carbon cycle and carbon storage of grassland.Therefore,soil bacterial community structure under a precipitation manipulation experiment was researched in a semi-arid desert grassland in Chinese Loess Plateau.Five precipitation levels,i.e.,control,reduced and increased precipitation by 40%and 20%,respectively(referred here as CK,DP40,DP20,IP40,and IP20)were set.The results showed that soil bacterial alpha diversity and rare bacteria significantly changed with altered precipitation,but the dominant bacteria and soil bacterial beta diversity did not change,which may be ascribed to the ecological strategy of soil bacteria.The linear discriminate analysis(LDA)effect size(LEfSe)method found that major response patterns of soil bacteria to altered precipitation were resource-limited and drought-tolerant populations.In addition,increasing precipitation greatly promoted inter-species competition,while decreasing precipitation highly facilitated inter-species cooperation.These changes in species interaction can promote different distribution ratios of bacterial populations under different precipitation conditions.In structural equation model(SEM)analysis,with changes in precipitation,plant growth characteristics were found to be drivers of soil bacterial community composition,while soil properties were not.In conclusion,our results indicated that in desert grassland ecosystem,the sensitive of soil rare bacteria to altered precipitation was stronger than that of dominant taxa,which may be related to the ecological strategy of bacteria,species interaction,and precipitation-induced variations of plant growth characteristics.

Phylogenetic diversity and specificity of bacteria associated with Microcystis aeruginosa and other cyanobacteria

Interactions between bacteria and cyanobacteria have been suggested to have a potential to influence harmful algal bloom dynamics; however, little information on these interactions has been reported. In this study, the bacterial communities associated with five strains of Microcystis aeruginosa, three species of other Microcystis spp., and four representative species of non-Microcystis cyanobacteria were compared. Bacterial 16S rDNA fragments were amplified and separated by denaturing gradient gel electrophoresis （DGGE） followed by DNA sequence analysis. The similarities among bacterial communities associated with these cyanobacteria were compared to the digitized DGGE profiles using the cluster analyses. The bacterial community structure of all cyanobacterial cultures differed. Cluster analysis showed that the similarity values among M. aeruginosa cultures were higher than those of other cyanobacterial cultures. Sequence analysis of DGGE fragments indicated the presence of bacteria including, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Bacteroidetes and Actinobacteria in the cyanobacterial cultures. Members of the Sphingomonadales were the prevalent group among the Microcystis-associated bacteria. The results provided further evidence for species-specific associations between cyanoabcteria and heterotrophic bacteria, which are useful for understanding interactions between Microcystis and their associated bacteria.

Rumen fermentation and bacterial communities in weaned Chahaer lambs on diets with different protein levels

We evaluatedthe effects of diets with different crude protein （CP） levels on growth performance, rumen fermentation and bacterial communities in weaned Chahaer lambs. 128 weaned Chahaer lambs （（20.56±1.43） kg body weight; ram：ewe 1：1） aged （61±1.85） d were randomly alotted to one of four diets with CP content of 11.17% （T1）, 12.06% （T2）, 13.40% （T3） or 14.36% （T4）.Ruminal fermentation parameters were measured and bacterial communities were analysed using PCR-dena-turing gradient gel electrophoresis （PCR-DGGE） and quantitative PCR. The average daily gain and feed utilization efifciency in T3 were higher than those in the other groups （P〈0.05）, although the dry matter intake and metabolizable energy intake were similar. Total volatile fatty acid concentration in the ruminal lfuid of T3 was lower than that of T1 （P=0.011）, T2 （P=0.008） or T4 （P=0.309）. The ammonia nitrogen concentration and acetate/propionate ratio of ruminal lfuid were signiifcantly higher in lambs fed the higher CP diets, whereas the molar concentrations of propionate and butyrate of ruminal lfuid were lower. The rumen bacterial community was similar in T2 and T3 which shown more stable and diverse rumen microbes ecosystem compared with the other groups. The DGGE proifles and phylogenetic tree indicated thatBacteroides uniformis,Clostrid-iumalkalicellulosi,Alkalibaculum bacchiandSaccharofermentanssp.were common bacterium of Chahaer lamb rumen. B. uniformis,C.alkalicelulosi,Saccharofermentanssp. andGracilibacter thermotolerans,which belong to the Bacteroidetes and Firmicutesphyla,were the dominant species in the rumen of lambs fed 13.40% CP.However,Ruminococcus albus, Ruminococcus lfavefaciensand Butyrivibrio ifbrisolvenswerenot differentin lambs fed different CP diets. Therefore, it could be concluded thatB. uniformis,C.alkalicelulosi,A. bacchiandSaccharofermentanssp.were common bacteria of Chahaer lamb rumen. Furthermore, the dietary CP of 13.04% could improve performance and change rumen fermentation model by increasing the dominant species’ peak intensities ofB. uniformis,C.alkalicelulosi,Saccharofermentanssp. and Gracilibacter thermotoleransand stabilizing rumen microbial ecosystem.

Bacterial and cyanobacterial diversities determined by T-RFLP analyses in the Jiaozhou Bay

The methods of DAPI staining epifluorescence microscopy and T-RFLP analysis were used to analyze the microbial abundance and diversity in surface seawater sampled from 12 stations inside and outside of the Jiaozhou Bay during a survey on 12 and 13 September 2004. The abundance of total microbes is in the range of 10^6～ 10^7 cells/cm^3, similar to those of most semi-enclosed bays in the temperate areas in the world. The highest microbial densities occur in the northeastern part of the Jiaozhou Bay, around the mouths of Loushan and Licun Rivers and the Hongdao aquacultural farming areas, suggesting that the degree and characteristics of pollutions, along with geographical and hydrological effects, may be important determinants affecting the abundance and distribution of bacteria in the Jiaozhou Bay. Bacterial communities inside and outside of the Jiaozhou Bay can be grouped into three classes based on T-RFLP patterns and cluster analyses. Stations at the water channel of the bay mouth and outside, such as D1, D3, D5, D6 and D7, are grouped together to stand for the outside bacterial community interacting with the environment outside of the Jiaozhou Bay. Stations of the innermost side of the Jiaozhou Bay, such as A3, A5, B2 and Y1, are grouped together to stand for the residential bacteria community. Stations C1, C3 and CA are grouped together and may stand for the transitional bacterial assemblage between the residential community and the outside community. However, there is no such a defined relationship for the case of cyanobacterial diversity, indicating the fact that cyanobacteria are more flexible and adaptable to all kinds of conditions.

Isolation and diversity analysis of heterotrophic bacteria associated with sea anemones

A study was undertaken to investigate the heterotrophic bacterial flora associated with the sea anemones. Samples of the sea anemones Anthopleura midori were collected from the coast of Weihai and bacteria were isolated from these samples. Additionally, high numbers of viable bacteria were obtained from the celom wall and surface of anemone, the community of cultivable bacteria was very diverse. As a result of this isolation, 60 strains were obtained, 56 of them were selected for identification and characterization by 16S rRNA gene sequence analysis and limited phenotypic testing. Among these isolates, 16 strains were phylogenetically related to members of the genus Pseudoalteromonas and neighboring taxa. Other isolates included members of the genera Colwcllia, Vibrio, Acinetobactcr, Pseudomonas, Endozoicomonas, Roseovarius, Paraeoceus, Loktanella, Leisingcra, Sulfitobacter, Bacillus, Staphylococcus, Plantibacter, Microbaeterium, Micro- coccus, Joostella, Psychroserpens, Cellulophaga, Krokinobaeter, Polaribacter and Psychrobaeter. Seven potential novel species were found. Among 60 strains, 17 of them can produce proteolytic exoenzyme, 20 can produce lipolytic exoenzyme. Strain NQ8 has strong antagonistic effects on some Vibrio strains. This study demonstrates that the culturable fraction of bacteria from the sea anemones Anthopleura midori is diverse and appears to possess much potential as a source for the discovery of novel bioactive materials.

Carbendazim induces a temporary change in soil bacterial community structure

The effect of carbendazim applications on the diversity and structure of a soil bacterial community was studied under field conditions using temperature gradient gel electrophoresis （TGGE） and partial sequence analysis of PCR-amplified 16S rRNA gene. After four successive introductions of carbendazim at a level of 0.94 kg active ingredient （a.i.）/ha, the genetic diversity （expressed as Shannon index, H′） decreased from 1.43 in the control to 1.29 in treated soil. This harmful effect seems to increase with the concentration of carbendazim. The value of H＇ in the soil treated with carbendazim at 4.70 kg a.i./ha was reduced to 1.05 （P ≤ 0.05）. The structure of soil bacterial community was also affected after four repeated applications of carbendazim at levels of 0.94, 1.88 and 4.70 kg a.i./ha, as seen in the relative intensities of the individual band. However, the bacterial community in carbendazim-treated soil recovered to that in the control 360 d after the first treatment. The results indicated that repeated applications of carbendazim could reduce soil microbial diversity and alter the bacterial community structure temporarily.

Diversity shifts of rumen bacteria induced by dietary forages in dairy cows and quantification of the changed bacteria using a new primer design strategy

The partial 16 S r RNA gene sequences（100 to 500 bp） were widely used to reveal rumen bacterial composition influenced by diets, while quantification of the changed uncultured bacteria was inconvenient due to difficult designing of specific primers based on short sequences. This study evaluated the effect of forage resources on rumen bacterial diversity and developed new strategy for primer design based on short sequences to quantify the changed uncultured bacteria. Denaturing gradient gel electrophoresis（DGGE） analysis and subsequent band sequencing were used to reveal the distinct rumen bacteria composition in cows fed with two forage sources（single corn stover vs. mixed forages including alfalfa hay and corn silage）. The bacterial diversity in the rumen of dairy cows fed with corn stover was lower than that with mixed forages（P0.05）. The bacterium named R-UB affiliating to uncultured Succinivibrionaceae was identified, and it was abundant in the rumen of cows fed with mixed forages compared to corn stover. The full length 16 S r RNA gene sequences with identity of 97% to the R-UB 16 S r RNA gene sequence were obtained from Gen Bank and used to design specific primers to quantify uncultured bacterium R-UB. All sequences of amplicon from the new primers were of 100% identity to R-UB sequences indicating the high specificity of new primers. Quantitative PCR confirmed that abundance of R-UB in the rumen of cows fed with corn stover was lower than those fed with mixed forages（P0.01）. New strategy for designing primers based on partial 16 S r RNA genes to quantify targeted uncultured bacteria was successfully developed. The rumen bacteria descending significantly in the cows fed corn stover compared to those fed mixed forages was identified as uncultured R-UB from Succinivibrionaceae.

Characterization of root-associated bacterial community structures in soybean and corn using locked nucleic acid(LNA) oligonucleotide-PCR clamping and 454 pyrosequencing

supported in part by grants from the Strategic Priority Research Program of Chinese Academy of Sciences （XDB15010103）;the National Natural Science Foundation of China （41201247）