Bacterial diversity in the sediments collected from the Shikoku Basin

Diversity of bacteria was studied in deep-sea sediments from the Shikoku Basin in the Northwest Pacific Ocean by PCR, RFLP and sequence analysis of 16S rDNA and comparing with Genbank database. Based on the RFLP profile generated, 77 clones from the 16S rDNA library were divided into 27 types. Phylogenetic analysis showed that the 27 independent clones fell into four groups: Proteobac-teria (62.96%), Chloroflexi (14.81%), Planctomycetes (14.81%) and Acidobacteria (7.41%). Among all sequenced clones, 6 were related to the sulfur or sulfate metabolism bacteria and the results also demonstrated that some bacteria in deep-sea sediments had relation to matter-energy circulation.

The diversity and potential function of endophytic bacteria isolated from Kobreasia capillifolia at alpine grasslands on the Tibetan Plateau, China

A total of 50 endophytic bacterial isolates were obtained from Kobreasia capillifolia at alpine grasslands in the Eastern Qilian Mountains on the Tibetan Plateau in China. Based on the sequencing and phylogenetic analysis of 16 S r DNA genes, all isolates phylogenetically related closely to Bacillus, Acinetobacter, Stenotrophomonas, Brevundimonas, Arthrobacter, Curtobacterium, Paenibacillus, Plantibacter, Promicromonospora, Serratia, and Microbacterium, among which Bacillus was the predominant genus（47.8% of the total number of endophytic isolates）. These isolates possessed different biological functions. In 50 endophytic bacteria, 42 isolates produced indole acetic acid（IAA） on King medium. There were seven isolates showing potency of mineral phosphate solubilization in Pikovaskaia＇s（PKO） liquid medium. Seven isolates exhibited antagonistic effect against Fusarium avenaceum, Colletotrichum coccodes and Phoma foveata. This was the first report on diversity and plant growth promotion of endophytic bacteria from K. capillifolia on alpine grassland in the Eastern Qilian Mountains, Chain. It is essential for revealing the relationship among plant, microorganism, and the special environment because the potential function of endophytic bacteria made a contribution to the interactions of plants and endophytic bacteria.

Responses of phytoplankton and its satellite bacteria to exogenous ethanol

The response of phytoplankton and its satellite bacteria to various concentrations(0.01%-10%v/v)of ethanol is studied.To elucidate the effect of ethanol,single-strains of phytoplankton(SSP)culture,pure strains of satellite bacteria isolated from nonaxenic SSP cultures,and Escherichia coli were screened.Results indicate that ethanol could promote the growth and photo synthetic efficiency(F_(v)/F_(m))of S SP at 0.01%and the growth of satellite bacteria at 0.01%-1%.Nevertheless,ethanol inhibited the growth and F_(v)/F_(m)of SSP at 0.1%-1%,and killed bacteria and SSP at 10% concentration.Further investigation on a satellite bacterium(Mameliella alba)revealed that ethanol promotes growth by serving as a growth stimulant rather than a metabolic carbon source.The 16 S rRNA gene amplicon indicated that all nonaxenic S SP cultures harbor distinct satellite bacteria communities where the SSP culture of Skeletonema costatum,Phaeodactylum tricornutum,and Dunaliella bardawil were dominated by bacteria genera of Marivita(~80%),Dinoroseobacter(~47%),and Halomonas(~87%),respectively,indicating that every SSP cultures have their own distinct satellite bacterial community.The bacteria family Rhodobacteraceae was dominant in the two marine diatoms,whereas Halomonadaceae was dominant in the saline green microalga.Compared to their respective controls,the supply of 0.5% ethanol to SSP cultures promoted the growth of the satellite bacteria but did not cause a significant difference in species composition of satellite bacteria.Therefore,a low concentration of ethanol can promote the growth of bacteria in a non-selective way.This study enriched our knowledge about the effect of ethanol on aquatic microbes and provided a baseline for basic and applied biotechnological re search in the aquatic environment in the future.

Comparison of rumen bacteria distribution in original rumen digesta, rumen liquid and solid fractions in lactating Holstein cows

Background： Original rumen digesta, rumen liquid and solid fractions have been frequently used to assess the rumen bacterial community. However, bacterial profiles in rumen original digesta, liquid and solid fractions vary from each other and need to be better established.Methods： To compare bacterial profiles in each fraction, samples of rumen digesta from six cows fed either a high fiber diet（HFD） or a high energy diet（HED） were collected via rumen fistulas. Rumen digesta was then squeezed through four layers of cheesecloth to separate liquid and solid fractions. The bacterial profiles of rumen original digesta, liquid and solid fractions were analyzed with High-throughput sequencing technique.Results： Rumen bacterial diversity was mainly affected by diet and individual cow（P 〉 0.05） rather than rumen fraction. Bias distributed bacteria were observed in solid and liquid fractions of rumen content using Venn diagram and LEf Se analysis. Fifteen out of 16 detected biomarkers（using LEf Se analysis） were found in liquid fraction, and these 15 biomarkers contributed the most to the bacterial differences among rumen content fractions.Conclusions： Similar results were found when using samples of original rumen digesta, rumen liquid or solid fractions to assess diversity of rumen bacteria; however, more attention should be draw onto bias distributed bacteria in different ruminal fractions, especially when liquid fraction has been used as a representative sample for rumen bacterial study.

Effect of salinity on community structure and naphthalene dioxygenase gene diversity of a halophilic bacterial consortium

The aim of this study is to analyze the effect of salinity on polycyclic aromatic hydrocarbons （PAHs） biodegradation, community structure and naphthalene dioxygenase gene （ndo） diversity of a halophilic bacterial consortium with the denaturing gradient gel electrophoresis （DGGE） approach. The consortium was developed from oil-contaminated saline soil after enrichment for six times, using phenanthrene as the substrate. The prominent species in the bacterial consortium at all salinities were identified as halophilic bacteria Halomonas, Alcanivorax, Marinobacter, Idiomarina, Martelella and uncultured bacteria. The predominant microbes gradually changed associating with the saline concentration fluctuations ranging from 0.1% to 25% （w/v）. Two ndo alpha subunits were dominant at salinities ranging, from 0.1% to 20%. while not been clearly detected at 25% salinity. Consistently. the biodegradation occurred at salmltles rangmg from 0.1% to 20%, while no at 25% salinity, suggesting the two ndo genes played an important role in the degradation. The phylogenetic analysis revealed that both of the two ndo alpha subunits were related to the classic nab-like gene from Pseudomonas stutzeri AN10 and Pseudomonas aeruginosa PaK1, while one with identity of about 82% and the other one with identity of 90% at amino acid sequence level. We concluded that salinity greatly affected halophilic bacterial community structure and also the functional genes which were more related to biodegradation.

A biogeographic map of soil bacterial communities in wheats field of the North China Plain

The vast diversity of soil bacteria provides essential ecosystem services that support agricultural production.Variation in the diversity and composition of soil biota may have predictive values for soil nutrient cycling and resilience of ecosystem services,thus providing valuable insights to improve food production.The North China Plain(NCP)is one of the world’s key agricultural regions,supplying more than 50% of the cereal consumed in Asia.However,it is unknown whether soil microbial diversity is predictable across the NCP.Using the MiSeq Illumina platform,we examined bacterial community variation in relation to spatial and environmental factors from 243 soils in wheat-maize double cropping rotation fields across the NCP,which cover nearly 0.3 million km^(2).Based on observed bacterial communities and their relationships with environmental factors,we generated a map of bacterial communities across the NCP.The highest bacterial diversity was found in the middle part of the NCP,with most of the variation in diversity attributable to differences in the community similarity of Actinobacteria and Alphaproteobacteria.These findings provide important baseline information for analyzing the relationships between microbial community,soil functionality and crop yields.

Identification and characterization of slime-producing microorganisms in papermaking water loops using emulsion polymerase chain reaction techniques

Slime formation on paper machines is a critical issue that can substantially impact the quantity and quality of paper production.This problem is caused by the growth of an abundant and diverse amount of bacteria.Through the application of emulsion polymerase chain reaction(emPCR),the bacterial diversity was analyzed on paper machines and more operational taxonomic units(OTUs)were obtained.Eleven types of bacterial phyla were found that have been previously identified,including Proteobacteria(α-,β-,γ-,ε-,andφ-),Bacteroidetes,Firmicutes,Cyanobacteria,Verrucomicrobia,Actinobacteria,Spirochaetes,Chloroflexi,Deinococcus-Thermus,and Armatimonadetes.Furthermore,for the first time,there were representatives of the phyla Lentisphaerae found on paper machines.This study revealed the wide bacterial diversities of slime found on paper machines in China,which was also similar to other industrial processes.