Impact of redox-stratification on the diversity and distribution of bacterial communities in sandy reef sediments in a microcosm

Relationships between microbial communities and geochemical environments are important in marine microbial ecology and biogeochemistry. Although biogeochemical redox stratification has been well documented in marine sediments, its impact on microbial communities remains largely unknown. In this study, we applied denaturing gradient gel electrophoresis (DGGE) and clone library construction to investigate the diversity and stratification of bacterial communities in redox-stratified sandy reef sediments in a microcosm. A total of 88 Operational Taxonomic Units (OTU) were identified from 16S rRNA clone libraries constructed from sandy reef sediments in a laboratory microcosm. They were members of nine phyla and three candidate divisions, including Proteobacteria (Alpha-, Beta-, Gamma-, Delta-, and Epsilonproteobacteria), Actinobacteria, Acidobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Firmicutes, Verrucomicrobia, Spirochaetes, and the candidate divisions WS3, SO31 and AO19. The vast majority of these phylotypes are related to clone sequences from other marine sediments, but OTUs of Epsilonproteobacteria and WS3 are reported for the first time from permeable marine sediments. Several other OTUs are potential new bacterial phylotypes because of their low similarity with reference sequences. Results from the 16S rRNA, gene clone sequence analyses suggested that bacterial communities exhibit clear stratification across large redox gradients in these sediments, with the highest diversity found in the anoxic layer (15–25 mm) and the least diversity in the suboxic layer (3–5 mm). Analysis of the nosZ, and amoA gene libraries also indicated the stratification of denitrifiers and nitrifiers, with their highest diversity being in the anoxic and oxic sediment layers, respectively. These results indicated that redox-stratification can affect the distribution of bacterial communities in sandy reef sediments.     

Molecular identification and culture trials of Eutreptiella gymnastica (Eutreptiales, Euglenophyceae)

During a survey for marine microalgal resources, we isolated a rare marine euglenoid from the coastal waters of Qingdao, China in 2009, and established a pure culture. Electron microscopic and molecular phylogenetic (18S rDNA and 16S rDNA sequences) analyses revealed a close affinity with Eutreptiella gymnastica, a bloom-forming species. Different culture conditions were monitored to understand optimal E. gymnastica growth characteristics. The optimal growth conditions in a batch culture of this isolate were 20°C, 160 μmol photons/(m2×s) of white light, and a salinity of 10-31. Nutrient experiments demonstrated that growth increased dramatically with a phosphorus concentration greater than 72 μmol/L. Understanding the effect of culture conditions on E. gymnastica may help understanding the blooming mechanism of this alga in its natural environment.     

Molecular phylogenetic analysis of attached Ulvaceae species and free-floating <Emphasis Type="Italic">Enteromorpha</Emphasis> from Qingdao coasts in 2007

Based on the sequence data of the nuclear ribosomal DNA internal transcribed spacer (ITS) 1, 5.8 S, and ITS 2, the molecular phylogeny was analyzed on Ulvaceae species collected from Qingdao coasts in summer of 2007, including 15 attached Ulva and Enteromorpha samples from 10 locations and 10 free-floating Enteromorpha samples from seven locations. The result supported the monophyly of all free-floating Enteromorpha samples, implying the unialgal composition of the free-floating Enteromorpha, and the attached Ulvaceae species from Qingdao coasts were grouped into other five clades, suggesting that they were not the biogeographic origin of the free-floating Enteromorpha in that season. Supported by NSFC (40506030); the Innovative Key Project of the Chinese Academy of Sciences (KZCX2-YW-209); Science & Technology Project of Qingdao City (06-2-2-12-JCH)     

Seasonal distribution of bioaerosols in the coastal region of Qingdao

Bioaerosols were collected by using a six-stage bioaerosols sampler from September 2007 to August 2008 in the coastal region of Qingdao, China. The terrestrial and marine microbes(including bacteria and fungi) were analyzed in order to understand the distribution features of bioaerosols. The results show that the average monthly concentrations of terrestrial bacteria, marine bacteria, terrestrial fungi and marine fungi are in the ranges of 80–615 CFU m-3, 91–468 CFU m-3, 76–647 CFU m-3 and 231–1959 CFU m-3, respectively. The concentrations of terrestrial bacteria, marine bacteria, terrestrial fungi, marine fungi and total microbes are the highest in each microbial category during fall, high in spring, and the lowest in the summer and winter. The bacterial particles are coarse in spring, autumn and winter. The sizes of fungal particle present the log-normal distribution in all the seasons.     

16S rRNA gene phylogenesis of culturable predominant bacteria from diseased Apostichopus japonicus (Holothuroidea, Echinodermata)

Cultured Apostichopus japonicus in China suffers from a kind of skin ulceration disease that has caused severe economic loss in recent years. The disease, pathogens of which are supposed to be bacteria by most researchers, is highly infectious and can often cause all individuals in the same culture pool to die in a very short time. The 16S rRNA gene phylogenesis of the culturable bacteria from the lesions of diseased individuals was conducted to study the biodiversity of the bacterial communities in the lesions and to identify probable pathogen(s) associated with this kind of disease. S. japonica samples were selected from a hatchery located in the eastern part of Qingdao, China. Bacterial universal primers GM5F and DS907R were used to amplify the 16S rRNA gene of bacteria colonies, and touchdown PCR was performed to amplify the target sequences. The results suggest that γ- proteobacteria (Alteromonadales and Vibrionales) of CFB group, many strains of which have been also determined as pathogens in other marine species, are the predominant bacterial genera of the diseased Apostichopus japonicus individuals.     

Construction of Porphyra yezoensis Pure Line from Protoplasts and Its 18S rDNA Sequence Determination

The wild Porphyra yezoensis collected from the Qingdao coast was used to prepare protoplasts by enzyme digestion. The pure line was constructed by cultivating the protoplasts. The 18S rDNA of the P. yezoensis pure line was cloned and sequenced. Sequence analysis was executed for this sequence and other 22 sequences retrieved from GenBank. A phylogenetic tree was constructed using the neighbor-joining method. The results revealed a high diversity of 18S rDNA sequences in genus Porphyra and the considerable variation of 18S rDNA sequences in different strains of the same species P. yezoensis and P. tenera. Significant difference of 18S rDNA sequence was observed between P. yezoensis from Qingdao, China, and the two strains of P. yezoensis from Japan, but the three strains of P. yezoensis formed a stable clade in the phylogenetic tree. These results indicate the possibility of interspecies and intraspecies discrimination of Porphyra using the 18S rDNA sequences.     

Heterotrophic bacterial floras in industrial area and unpolluted marine environments around Qingdao

From Oct. 1999 to Oct. 2000, the heterotrophic bacterial floras in the industrial marine environment around the Qingdao Power Plant (QPP) and in the unpolluted marine environments were investigated. The results showed that the numbers of the heterotrophic bacteria around QPP were much higher than those in unpolluted environments, and the average numbers in QPP Seawater, QPP Sediment, Unpolluted Seawater and Unpolluted Sediment were 5.4×10⁴cfu(mL)⁻¹, 5.0×10⁵cfug⁻¹, 3.0×10²cfu(mL)⁻¹ and 1.3×10⁵cfug⁻¹ respectively. Totally, 118 strains were isolated from QPP and 99 of them were Gram-negative. One hundred and twenty one strains were isolated from the unpolluted environments and 104 of them were Gram-negative. All the Gram-negative bacteria belonged to 13 genera. The distribution of the bacteria was varied in different marine environments. The results showed that the unpolluted marine environments contained much more Vibrio than seawater and sediment around QPP.     

Characterization of Bioaerosol Bacterial Communities During Hazy and Foggy Weather in Qingdao,China

This study was conducted to evaluate the impact of hazy and foggy weather on the bacterial communities in bioaerosols, for which samples were collected from the Qingdao coastal region on sunny, foggy, and hazy days in January and March 2013. Bacterial community compositions were determined using polymerase chain reaction denaturing gradient gel electrophoresis (PCRDGGE). The bacterial community diversity was found to be high on foggy and hazy days, and the dominant species differed during hazy weather. The Shannon-Wiener index revealed that the bacterial community diversity of coarse particles was higher than that of fine particles in the bioaerosols. The bacterial community diversity of fine particles significantly correlated with relative humidity (RH; r² = 0.986). The cluster analysis results indicated that the bacterial communities on sunny days differed from those on hazy and foggy days. Compared with sunny days, the bacterial communities in the fine particles during hazy weather exhibited greater changes than those in the coarse particles. Most of the sequenced bacteria were found to be closely affiliated with uncultured bacteria. During hazy weather, members of the classes Bacilli and Gammaproteobacteria (Pseudomonas and Acinetobacter) were dominant. The DGGE analysis revealed that Proteobacteria and Firmicutes were the predominant phyla, and their relative percentages to all the measured species changed significantly on hazy days, particularly in the fine particles. Haze and fog had a significant impact on the bacterial communities in bioaerosols, and the bacterial community diversity varied on different hazy days.     

Microbial ecological associations in the surface sediments of Bohai Strait

Microbial communities play key roles in the marine ecosystem. Despite a few studies on marine microbial communities in deep straits, ecological associations among microbial communities in the sediments of shallow straits have not been fully investigated. The Bohai Strait in northern China(average depth less than 20 m) separates the Bohai Sea from the Yellow Sea and has organic-rich sediments. In this study, in the summer of 2014, six stations across the strait were selected to explore the taxonomic composition of microbial communities and their ecological associations. The four most abundant classes were Gammaproteobacteria, Deltaproteobacteria, Bacilli and Flavobacteriia. Temperature, total carbon, depth, nitrate, fishery breeding and cold water masses influenced the microbial communities, as suggested by representational dif ference and composition analyses. Network analysis of microbial associations revealed that key families included Flavobacteriaceae, Pirellulaceae and Piscirickettsiaceae. Our findings suggest that the families with high phylogenetic diversity are key populations in the microbial association network that ensure the stability of microbial ecosystems. Our study contributes to a better understanding of microbial ecology in complex hydrological environments.     

PCR-DGGE analysis of intestinal bacteria and effect of Bacillus spp. on intestinal microbial diversity in kuruma shrimp (Marsupenaeus japonicus)

In this study, the intestinal microbiota of kuruma shrimp (Marsupenaeus japonicus) was examined by molecular analysis of the 16S rDNA to identify the dominant intestinal bacteria and to investigate the effects of Bacillus spp. on intestinal microbial diversity. Samples of the intestines of kuruma shrimp fed normal feed and Bacillus spp. amended feed. PCR and denaturing gradient gel electrophoresis (DGGE) analyses were then performed on DNA extracted directly from the guts. Population fingerprints of the predominant organisms were generated by DGGE analysis of the universal V3 16S rDNA amplicons, and distinct bands in the gels were sequenced. The results suggested that the gut of kuruma shrimp was dominated by Vibrio sp. and uncultured gamma proteobacterium. Overall, the results of this study suggest that PCR-DGGE is a possible method of studying the intestinal microbial diversity of shrimp.     

Salinity tolerance and genetic diversity of the dinoflagellate <Emphasis Type="Italic">Oxyrrhis marina</Emphasis>

To evaluate the relationship between salinity tolerance and genetic diversity of plankton, we collected a wild species of plankton from Taipingjiao, Qingdao. The fragment of ITS1-5.8S rDNA-ITS2 was extracted and sequenced. The results showed that the plankton belongs to Oxyrrhis marina. The salinity tolerance of O. marina ranges from 4 to 60. Seven selected groups were built up to evaluate salinity tolerance and to assess genetic diversity by RAPD. The salinity tolerance comparison revealed considerable differences among groups: the strains of O. marina in group 4 could survive under salinity from 4 to 32, while the strains selected for salinity 60 died under the salinity lower than 16. Analysis of genetic diversity of the seven groups showed that the mean genetic diversity index value was 0.28, but it was only 0.16 in selected group of 4 and was 0.24 for group 60. The result of AMOVA suggested a significantly positive relationship between the salinity tolerance and genetic diversity of O. marina (P<0.01). This study indicates that consideration of intraspecific genetic divergence in O. marina might be indispensable when using it as a model in the study of salinity tolerance of wild plankton.     

Variations of bacterial and fungal communities along a primary successional chronosequence in the Hailuogou glacier retreat area (Gongga Mountain,SW China)

New terrestrial habitats have emerged and a primary succession has developed in the retreat area(29°34'N, 102°00'E, 2951–2886 m) after the retreat of the Hailuogou glacier. To investigate soil microbial changes along the primary successional chronosequence, mixed soil samples were collected at six sites at different ages(2 young sites, 2 mid-aged sites, and 2 old sites). The RNA was extracted and amplified. Bacterial 16 S r RNA and fungal 18 S r RNA were analyzed using high-throughput 454 pyrosequencing analysis. Overall, pyrosequencing showed that Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria were the main bacterial phyla, and the fungal communities were strongly dominated by the phyla Ascomycota and Basidiomycota in the retreat area. The Shannon diversity index(Hshannon) of bacteria was 6.5 – 7.9, and that of fungi was 2.2 – 4.1 in these sites. For the bacterial communities, diversity and evenness values were highest on the mid-age sites and wererelatively low on the young and old sites. A similar trend was observed for the fungal communities. In contrast, soil properties showed significant linear distributional trends(increase or decrease) with the age of the site. Combining the linear change patterns of soil properties, the highest values of bacterial and fungal evenness and diversity in the mid-aged sites indicated that there was less environmental stress and more niches for microbial communities in the middle successional stage compare with other stages. In addition, our analysis showed that microbial communities were the main drivers that build a soil organic matter pool to expedite pedogenesis for ecosystem succession. This primary succession in the Hailuogou glacier retreat area is developing rapidly compared with that in other glacier retreats.     

Otolith chemical signatures of spottedtail goby Synechogobius ommaturus in coastal waters of China

This study explores the potential existence of local stocks of Synechogobius ommaturus using otolith chemical signatures. The concentrations of 10 elements (K, Ca, Na, Mg, Sr, Pb, Ba, Mn, Co, Zn) in the otoliths from eight stocks (Dandong, Dalian, Tianjin, Dongying, Weihai, Qingdao, Ganyu and Xiamen) of S. ommaturus were measured by Inductively Coupled Plasma Mass Spectrometry and regressed against otolith weight. No significant correlation between otolith weight and concentrations of Na, Mg, Ca, Sr, Co, Ba, Zn and Pb were observed. Concentrations of K and Mn were correlated with otolith weight. Consequently, the residuals of the regressions were used instead of the original concentrations in subsequent analyses. Analysis of variance (ANOVA) showed no significant difference between males and females in otolith chemical signatures. Differences were found among the locations for K, Sr, Mn, Co, Ba, Pb, but not for Ca, Na, Mg and Zn. Residuals of the regressions of elemental concentrations against otolith weight that fitted the normal distribution and homogeneity were studied by discriminant analysis. The success of the discriminant function to predict the location of S. ommaturus capture ranged from 100% for Weihai and Xiamen stocks, to only 44.4% and 62.5% for Qingdao and Dandong stocks, respectively. The average prediction success was 80.3%.     

Structure and diversity dynamics of microbial communities at day and night: investigation of meromictic Lake Doroninskoe,Transbaikalia, Russia

Extreme environmental conditions are key factors in the formation of the structure and diversity of microbial communities. In meromictic ecosystems, extreme conditions and a stable stratification of physical, chemical and biological parameters lead to diversity and heterogeneity of microenvironments. Lake Doroninskoe is located in an extreme geographical area and diff ers from other known meromictic reservoirs of the world by a low level of illumination in the chemocline and a rare type of alkaline water in sedimentary rocks formed by evaporative concentration. To understand the key factors that shape the composition and structure of the microbial community, the macro-and micro-variations in space and time are of great importance. We investigated the short-term dynamics of the structure and diversity of microbial communities of the meromictic soda lake, Lake Doroninskoe, at day and night using highthroughput sequencing and bioinformatics. Metagenomic analysis of 16 S rRNA gene amplicons showed that the microbial communities had a high taxonomic diversity both at day and night. Sixteen bacterial and three archaeal phyla were identified. Proteobacteria were dominant and comprised 75% during the day, increasing to 90% at night. Metabolically stable denitrifying bacteria that were able to use a variety of alternative electron acceptors and electron donors were prevalent in Lake Doroninskoe. They belonged to the families Enterobacteriaceae(class Gammaproteobacteria) and Alcaligenaceae(class Betaproteobacteria). Statistically significant differences between day and night microbial communities were found. During the day, the microbial community was the most diverse. We discuss the peculiarities of the underexplored shortterm dynamics of the structure and diversity of the microbial communities of the meromictic soda Lake Doroninskoe, and propose topics for prospective studies.     

Microbial communities present on mooring chain steels with different copper contents and corrosion rates

Copper has long been utilized as a disinfectant for bacteria,but its impact on microbial communities attached to the steel surface in seawater remains unknown.In the present study,3 mooring chain steels of different copper contents are subjected to a 3-month marine field exposure,and the corrosion rate increases in the order of BR5 steel(without copper) BR5 CuH steel(0.8% copper) BR5 CuL steel(0.4% copper).The microbial community results show that copper introduction does not result in an obvious change in microbial quantity,but it alters the diversity,richness,and structure of microbial communities due to the variation in copper-resistance of different species.BR5 CuH steel holds microbial communities with the highest percentage of some well-known corrosive microbes including sulfate-reducing bacteria,sulfuroxidizing bacteria,and iron-oxidizing bacteria,but possesses the lowest community diversity/richness owing to the toxicity of copper.The microbial community diversity/richness is stimulated by the low-copper content of BR5 CuL steel,and this steel also carries an intermediate proportion of such corrosive bacteria.Both well-known corrosive bacteria and microbial community diversity/richness seem to be involved in the corrosion acceleration of copper-bearing mooring chain steels.     

The levels of microbial diversity in dif ferent water layers of saline Chagan Lake,China

Saline lakes represent a particularly interesting aquatic environment for harboring high microbial diversity.However,the microbial diversity in different states and locations of saline lake is often overlooked.We studied for the first time the diversity and relative composition of the microbial communities in the Chagan Lake,NE China,and investigated the dif ferences in microbial species and physical and chemical factors in different geographical localities of the lake.After extracting the total DNA of the sample,we tested the library with the established library,sequenced the qualified library with Illumina HiSeq 2500,and studied the bacterial diversity by 16 S rRNA targeted metagenomics analysis.Results reveal that the highest microbial abundance in Chagan Lake at genus level was Proteobacterium followed by Actinomycetes and Bacteroides.In addition,we compared the microbial composition within the lake using alpha-and beta-diversity indices,showing that both diversity and evenness were the highest in the middle of the lake and lowest in the west of lake areas,and in the upper,middle,and lower depth of water columns,the low water column had the highest species number in the whole water environment,but the dif ference was not significant.We believe that physicochemical factors contribute to the formation of microbial community composition and diversity.In aquaculture industry,it is impossible apply horticulture for making full use of the spatial dif ferences in the microbial composition of the water.Therefore,combining cultured aquatic animal with the most suitable microbial species is a good way to boost the breeding ef fect for greater economic value.     

First Record and Redefinition of the Qingdao Population of Marine Ciliate Cardiostomatella vermiformis （Kahl, 1928） Corliss, 1960 （Protozoa, Ciliophora）

The living morphology and infraciliature of a marine ciliate, Cardiostomatella vermiformis isolated from a sand beach of the Jiaozhou Bay near Qingdao, China, were investigated by live observation, protargol and silver carbonate impregnation methods. Both the morphological and morphometric data largely agree with former records. Based on the data obtained, an improved diagnosis for Cardiostomatella vermiformis is supplied: Large marine Cardiostomatella with cylindrical body shape and several prolonged caudal cilia; cells in vivo about (90–500) μm×(30–120) μm; macronucleus beaded; single contractile vacuole caudally positioned; buccal apparatus conspicuously small, genus typical; three to six postoral kineties; 96-130 somatic kineties. This species is recorded for the first time in China.     

Exopolysaccharide production by four cyanobacterial isolates and preliminary identification of these isolates

Four marine cyanobacterial isolates, named 104, 109, 113 and 115, from marine water off China＇s coast can release a large amount of exopolysaccharide （EPS） to medium. The effects of different components in medium on EPS production by the four isolates were investigated. Under the optimal condition, the EPS released by isolates 104,109, 113 and 115 reached 7.48 g L^-1, 8.33 g L^-1, 18.26 g L^-1, and 6.78 g L^-1 within 14 d,respectively. Based on the conventional identification methods for cyanobacteria,these isolates were assigned to genus Cyanothece.     

Sediment flux and source in northern Yellow Sea by^210 Pb technique

1 INTRODUCTION The Yellow Sea is a shallow epicontinental sea surrounded by Chinese mainland and Korean Peninsula. It is connected with the East China Sea to the south, and with the Bohai Sea to the north- west. Water depth is generally less than 80 m with average of 44 m (Qin et al., 1989). The major sediment sources are the Huanghe and Changjiang (Yangtze) Rivers, providing annual sediment load of about 1.1×109 and 4.9×108 tons, respectively. A maximum of 1.6×108 tons of sedime…     

Amylase production by the marine yeast Aureobasidium pullulans N13d

The marine yeast strain N13d, producing an extracellular amylase, was isolated from the deep sea sediments of the Pacific Ocean. This strain was identified to be Aureobasidium pullulans by 18S rRNA gene sequence analysis and routine yeast identification methods. The optimal sea water medium for amylase production by this yeast strain was 1.0% peptone and 1.0% soluble starch with pH 4.0. The optimal conditions for amylase production by this yeast strain were with temperature 28 °C, aeration rate 6 Lmin⁻¹ and agitation speed 250 rmin⁻¹. Under these conditions, 58.5 units of amylase activity per mg protein were produced within 56 h of fermentation.