Analysis of cultivable aerobic bacterial community composition and screening for facultative sulfate-reducing bacteria in marine corrosive steel

Anaerobic, aerobic, and facultative bacteria are all present in corrosive environments. However, as previous studies to address corrosion in the marine environment have largely focused on anaerobic bacteria, limited attention has been paid to the composition and function of aerobic and facultative bacteria in this process. For analysis in this study, ten samples were collected from rust layers on steel plates that had been immersed in seawater for diff erent periods (i.e., six months and eight years) at Sanya and Xiamen, China. The cultivable aerobic bacterial community structure as well as the number of sulfate-reducing bacteria (SRB) were analyzed in both cases, while the proportion of facultative SRB among the isolated aerobic bacteria in each sample was also evaluated using a novel approach. Bacterial abundance results show that the proportions are related to sea location and immersion time;abundances of culturable aerobic bacteria (CAB) and SRB from Sanya were greater in most corrosion samples than those from Xiamen, and abundances of both bacterial groups were greater in samples immersed for six months than for eight years. A total of 213 isolates were obtained from all samples in terms of CAB community composition, and a phylogenetic analysis revealed that the taxa comprised four phyla and 31 genera. Bacterial species composition is related to marine location;the results show that Firmicutes and Proteobacteria were the dominant phyla, accounting for 98.13% of the total, while Bacillus and Vibrio were the dominant genera, accounting for 53.06% of the total. An additional sixfacultative SRB strains were also screened from the isolates obtained and were found to encompass the genus Vibrio (four strains), Staphylococcus (one strain), and Photobacterium (one strain). It is noteworthy that mentions of Photobacterium species have so far been absent from the literature, both in terms of its membership of the SRB group and its relationship to corrosion.

Spatial distribution characteristics of bacterial community structure and gene abundance in sediments of the Bohai Sea

This study investigated differences in the community structure and environmental responses of the bacterial community in sediments of the Bohai Sea.Illumina high-throughput sequencing technology and real-time PCR were used to assay the bacterial 16S rRNA genes in the surface sediments of 13 sampling stations in the Bohai Sea.The results showed that sediments at the majority of the 13 sampling stations were contaminated by heavy metal mercury.The main phyla of bacteria recorded included Proteobacteria(52.92%),Bacteroidetes(11.76%),Planctomycetes(7.39%),Acidobacteria(6.53%)and Chloroflexi(4.97%).The genus with the highest relative abundance was Desulfobulbus(4.99%),which was the dominant genus at most sampling stations,followed by Lutimonas and Halioglobus.The main factors influencing bacterial community structure were total organic carbon,followed by depth and total phosphorus.The content of lead,cadmium,chromium,copper and zinc had a consistent effect on community structure.Arsenic showed a negative correlation with bacterial community structure in most samples,while the impact of mercury on community structure was not significant.The bacterial community in sediment samples from the Bohai Sea was rich in diversity and displayed an increase in diversity from high to low latitudes.The data indicated that the Bohai Sea had abundant microbial resources and was rich in bacteria with the potential to metabolize many types of pollutants.

Response of microbial biomass and bacterial community composition to fertilization in a salt marsh in China

The effects of nitrogen （N） addition on microbial biomass, bacterial abundance, and community composition in sediment colonized by Suaeda heteroptera were examined by chloroform fumigation extraction method, real-time quantitative polymerase chain reaction, and denaturing gradient gel electrophoresis （DGGE） in a salt marsh located in Shuangtai Estuary, China. The sediment samples were collected from plots treated with different amounts of a single N fertilizer （urea supplied at 0.1, 0.2, 0.4 and 0.8 g/kg （nitrogen content in sediment） and different forms of N fertilizers （urea, （NH4）2SO4, and NH4NO3, each supplied at 0.2 g/kg （calculated by nitrogen）. The fertilizers were applied 1-4 times during the plant-growing season in May, luly, August, and September of 2013. Untreated plots were included as a control. The results showed that both the amount and form of N positively influenced microbial biomass carbon, microbial biomass nitrogen, and bacterial abundance. The DGGE profiles revealed that the bacterial community composition was also affected by the amount and form of N. Thus, our findings indicate that short-term N amendment increases microbial biomass and bacterial abundance, and alters the structure of bacterial community.

Effects of enrichmemt planting with native tree species on bacterial community structure and potential impact on Eucalyptus plantations in southern China

Multi-generational planting of Eucalyptus species degrades soil quality but the introduction of legumes can improve soil fertility and microbial diversity.However,the effects of introducing non-legume native tree species on soil nutrients and bacterial community structure remain poorly understood.This study investigated the impacts of the conversion of third generation monoculture Eucalyptus plantations to mixed systems including Eucalyptus urograndis with Cinnamomum camphora(EC)and E.urograndis with Castanopsis hystrix(EH),on soil chemical and biochemical properties and bacterial community structure,diversity and functions.First generation E.urophylla plantations were the control.Results show that planting the third generation Eucalyptus led to a significant decrease in p H,organic matter,nutrient content,enzyme activities(invertin,acid phosphataes,and urease),and bacterialα-diversity compare to the controls.However,the mixed planting showed significant improvement in soil chemical and biochemical attributes and bacterialα-diversity,although the E.urograndis and C.hystrix planting had no improvement.Chloroflexi(oligotrophic bacteria)were significantly enriched in third generation Eucalyptus and Eucalyptus+C.hystrix,while proteobacteria increased significantly in the E.urograndis with C.camphora plantings.The relative abundance of multiple metabolic pathways increased significantly in the third generation Eucalyptus plantations whereas membrane transportrelated genes were enriched in soils of the mixed systems.The changes in bacterial community structures in the two mixed systems were driven by diversity,organic matter and acid phosphatase,while bacterial functions were affected by invertase,NO_(3)^(-)-N,diversity and urease.These results suggest that the transformation of successive monoculture Eucalyptus plantations into mixed plantations reduces the depletion of soil nutrients and enhances the ecological function of soil microorganisms.

Distribution of Bacterial Communities in Petroleum-Contaminated Soils from the Dagang Oilfield, China

Diversity in bacterial communities was investigated along a petroleum hydrocarbon content gradient(0-0.4043 g/g)in surface(5-10 cm)and subsurface(35-40 cm)petroleum-contaminated soil samples from the Dagang Oilfield,China.Using 16S rRNA Illumina high-throughput sequencing technology and several statistical methods,the bacterial diversity of the soil was studied.Subsequently,the environmental parameters were measured to analyze its relationship with the community variation.Nonmetric multidimensional scaling and analysis of similarities indicated a significant difference in the structure of the bacterial community between the nonpetroleum-contaminated surface and subsurface soils,but no differences were observed in different depths of petroleum-contaminated soil.Meanwhile,many significant correlations were obtained between diversity in soil bacterial community and physicochemical properties.Total petroleum hydrocarbon,total organic carbon,and total nitrogen were the three important factors that had the greatest impacts on the bacterial community distribution in the long-term petroleum-contaminated soils.Our research has provided references for the bacterial community distribution along a petroleum gradient in both surface and subsurface petroleum-contaminated soils of oilfield areas.

应用PCR-DGGE技术分析福州左海湖的细菌群落组成

应用PCR-DGGE技术对4个月份(2011年12月、2012年2月、4月、6月)的福州左海湖细菌群落组成和优势菌群进行分析,研究结果发现相同月份4个采样点的DGGE图谱差异性不大,细菌群落组成具有较高的相似性;而不同月份4个采样点的DGGE条带的数目和位置表现出明显差异,细菌群落组成差异明显。对20条不同位置的DGGE条带进行切胶回收、扩增和测序后,进行系统进化分析,结果显示这20条带归属于4个细菌类群,即变形菌门Proteobacteria、拟杆菌门Bacteroidetes、放线菌门Actinobacteria、蓝细菌门Cyanobacteria。20条序列中有11条鉴定为变形细菌门Proteobacteria、5条鉴定为拟杆菌门Bacteroidetes、2条鉴定为放线菌门Actinobacteria、其余2条属于蓝细菌门Cyanobacteria。研究结果表明,左海湖细菌群落组成包括了Proteobacteria、Bacteroidetes、Actinobacteria、Cyanobacteria,其中以Proteobacteria为优势菌群。

Screening and degrading characteristics and community structure of a high molecular weight polycyclic aromatic hydrocarbon-degrading bacterial consortium from contaminated soil

Inoculation with efficient microbes had been proved to be the most important way for the bioremediation of polluted environments. For the treatment of abandoned site of Beijing Coking Chemical Plant contaminated with high level of high-molecular-weight polycyclic aromatic hydrocarbons （HMW-PAHs）, a bacterial consortium capable of degrading HMW-PAHs, designated 1-18-1, was enriched and screened from HMW-PAHs contaminated soil. Its degrading ability was analyzed by high performance liquid chromatography （HPLC）, and the community structure was investigated by construction and analyses of the 16S rRNA gene clone libraries （A, B and F） at different transfers. The results indicated that 1-18-1 was able to utilize pyrene, fluoranthene and benzo[a]pyrene as sole carbon and energy source for growth. The degradation rate of pyrene and fluoranthene reached 82.8% and 96.2% after incubation for 8 days at 30℃, respectively; while the degradation rate of benzo[a]pyrene was only 65.1% after incubation for 28 days at 30℃. Totally, 108, 100 and 100 valid clones were randomly selected and sequenced from the libraries A, B, and E Phylogenetic analyses showed that all the clones could be divided into 5 groups, Bacteroidetes, ct-Proteobacteria, Actinobacteria, β-Proteobacteda and γ- Proteobacteria. Sequence similarity analyses showed total 39 operational taxonomic units （OTUs） in the libraries. The predominant bacterial groups were α-Proteobacteria （19 OTUs, 48.7%）, γ-Proteobacteria （90TUs, 23.1%） and β-Proteobacteria （80TUs, 20.5%）. During the transfer process, the proportions of α-Proteobacteria and β-Proteobacteria increased greatly （from 47% to 93%）, while γ-Proteobacteda decreased from 32% （library A） to 6% （library F）; and Bacteroidetes group disappeared in libraries B and F.

Effect of reclaimed water effluent on bacterial community structure in the Typha angustifolia L. rhizosphere soil of urbanized riverside wetland, China

In order to evaluate the impact of reclaimed water on the ecology of bacterial communities in the Typha angustifolia L. rhizosphere soil, bacterial community structure was investigated using a combination of terminal restriction fragment length polymorphism and 16S rRNA gene clone library. The results revealed significant spatial variation of bacterial communities along the river from upstream and downstream. For example, a higher relative abundance of γ-Proteobacteria, Firmicutes, Chloroflexi and a lower proportion of β-Proteobacteria and ε-Proteobacteria was detected at the downstream site compared to the upstream site. Additionally, with an increase of the reclaimed water interference intensity, the rhizosphere bacterial community showed a decrease in taxon richness, evenness and diversity. The relative abundance of bacteria closely related to the resistant of heavy-metal was markedly increased, while the bacteria related for carbon/nitrogen/phosphorus/sulfur cycling wasn＇t strikingly changed. Besides that, the pathogenic bacteria markedly increased in the downstream rhizosphere soil since reclaimed water supplement, while the possible plant growth-promoting rhizobacteria obviously reduced in the downstream sediment. Together these data suggest cause and effect between reclaimed water input into the wetland, shift in bacterial communities through habitat change, and alteration of capacity for biogeochemical cycling of contaminants.

Bacterial diversity and distribution in the southeast edge of the Tengger Desert and their correlation with soil enzyme activities

The nature of microbial communities and their relation to enzyme activities in desert soils is a neglected area of investigation. To address this, the bacterial diversity and distribution and soil physico-chemical factors were investigated in the soil crust, the soil beneath the crust and rhizosphere soil at the southeast edge of the Tengger Desert, using the denaturing gradient gel electrophoresis of 16S rRNA genes amplified by the polymerase chain reaction. Phylogenedc analysis of the sequenced DGGE bands revealed a great diversity of bacteria. The Proteobacteria, consisting of the α, β, and γsubdivisions, were clearly the dominant group at all depths and in rhizosphere soil. Analysis of the enzyme activities indicated that the rhizosphere soil of Caragana korshinskii exhibited the highest protease and polyphenol oxidase activities, and in the soil crust there were increased activities of catalase, urease, dehydrogenase and sucrase. The bacterial community abundance closely correlated with soil enzyme activities in different soils. The presence of Cyanobacteria correlated with significant increases in protease, catalase and sucrase in the soil crust, and increased urease in the rhizosphere soil of Artemisia ordosica. The occurrence of Acidobacteria was associated with significant increases in urease, dehydrogenase, and sucrase in the rhizosphere soil of C. korshinski. The presence of γ-Proteobacteria correlated with a significant increase in polyphenol oxidase in the rhizosphere soil ofA. ordosica. The study indicated a close relationship between the soil bacterial community and soil enzymes, suggesting the necessity of further investigations into bacterial function in this desert ecosystem.

The microbiota in spider mite feces potentially reflects intestinal bacterial communities in the host

Microorganisms prov ide many physiological functions to herbivorous hosts.Spider mites(genus Tetranychus)are important agricultural pests throughout the world;however,the composition of the spider mite microbial community,especially gut micro-biome,remains unclear.Here,we investigated the bacterial community in five spider mite species and their associated feces by deep sequencing of the 16S rRNA gene.The composi-tion of the bacterial community was significantly different among the five prevalent spider mite species,and some bacterial symbionts showed host-species specificity.Moreover,the abundance of the bacterial community in spider mite feces was significantly higher than that in the corresponding spider mite samples.However,Flavobacterium was detected in all samples,and represent a"core microbiome".Remarkably,the maternally inherited endosymbiont Wolbachia was detected in both spider mite and feces.Overall,these results offer insight into the complex community of symbionts in spider mites,and give a new direction for future studies.

Bacterial communities associated with natural and commercially grown rooibos (Aspalathus linearis)

Aspalathus linearis is a commercially important plant species endemic to the Cape Floristic Region of South Africa and is used to produce a herbal tea known as rooibos tea.Symbiotic interactions between A.linearis and soil bacteria play an important role in the survival of Aspalathus plants in the highly nutrient-poor,acidic fynbos soil.The aim of this study was to characterize and compare rhizosphere and bulk soil bacterial communities associated with natural and commercially grown A.linearis,as well as the effect of seasonal changes on these communities.Bacterial communities were characterized using high throughput amplicon sequencing,and their correlations with soil chemical properties were investigated.The N-fixing bacterial community was characterized using terminal restriction fragment length polymorphism and real time quantitative polymerase chain reaction.Actinobacteria,Proteobacteria,and Acidobacteria were the most dominant bacterial phyla detected in this study.Highly similar bacterial communities were associated with natural and commercially grown plants.Significant differences in the bacterial community were observed between rhizosphere and bulk soils collected in the dry season,while no significant differences were detected in the wet season.This study provides insights into bacterial community structure and potential factors shaping bacterial community structure with commercially important A.linearis.

Catalog of operational taxonomic units and unified amplicon sequencing data for the microbiomes of medicinal plant roots

China has a rich history of cultivating medicinal plants,whose root microbial communities closely interact with the medicinal plants,thereby influencing their growth,health,and medicinal properties.Currently,researchers widely use 16S rRNA gene amplicon sequencing to study these root microbial communities.However,publicly available sequence datasets often lack essential sample information or contain errors,impeding the reuse of the datasets in the future.In this study,we aimed to create a united,reliable,and readily usable source of 16S rRNA gene sequences for medicinal plant root microbiomes.We compiled a catalog of 1392 microbiome samples for 58 medicinal plants from 58 studies,and manually provided essential sample information based on the experimental setup described in the associated papers.We then processed the sequences using a custom pipeline,generating a united catalog of operational taxonomic units(OTUs)and conducting taxonomic classification.We also pre-dicted the ecological functions of the communities for each sample.Finally,we used this dataset,to compare the rhizosphere bacterial communities of Pseudostellaria heterophylla from Fujian and Guizhou Provinces,revealing significant differences in the community composition of the same plant from different geographic locations.By providing a comprehensive and united catalog of amplicon sequences and OTUs for medicinal plant root bacterial communities,this study offers an invaluable resource for future comparative studies and data mining.