Spatial distribution and structure of benthic polychaete communities of Essaouira intertidal rocky shores (Atlantic coast of Morocco)

Polychaetes are one of the most important groups of macrobenthic organisms in coastal and marine environments, in terms of diversity and abundance, and play an important role in the functioning of ecosystem. This study aims to describe the structure and spatial distribution of polychaete communities along Essaouira's rocky shoreline(Atlantic coast of Morocco) in relation to the major environmental variables such as granulometry, salinity, temperature, pH, and intertidal range. Twelve sites from these intertidal rocky shores were sampled using a quadrat method during the summer 2016. A total of 4 435 individuals belonging to 34 taxa were recorded. Among the families, Sabellaridae(24%) and Nereididae(23%) were ranked ?rst in terms of abundance of individuals. Sabellaria alveolata(24%) and Perinereis cultrifera(13%) were the dominant species. Diversity( H′) values varied from 2.28 to 3.95. Pielou's index( J′) varied between 0.62 and 0.89. This was essentially due to the low dominance of few species. Cluster analysis was used to characterise Essaouira's rocky shores on the basis of benthic polychaete communities. SIMPER analysis con?rmed the presence of three distinct communities. According to canonical correspondence analysis, the structure and distribution of faunal assemblages of benthic polychaetes was mainly related to topographical complexity, water temperature, hydrodynamic conditions and upwelling. We conclude that these rocky shores show typically high benthic polychaete diversity compared to the taxonomic list of other rocky coasts. In addition, these results constitute a baseline data for the development of a sustainable network for long-term monitoring of benthic polychaete community changes due to ecological factor in?uences and anthropogenic activity impacts.     

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.     

Nematode diversity of Qingdao coast inferred from the 18S ribosomal RNA gene sequence analysis

The 18S ribosomal DNA gene （18S rDNA） sequences （approxtmately 1300 bp in length） were amplified from the DNA extracted from the free-living marine nematodes collected from the inter-tidal sediment of Qingdao coast in bulk with nematode specific primers. The PCR products were cloned, re-amplified, digested with Rsa I and Hin61 restriction endonucleases and separated in agarose gel. Among 17 restriction fragment length types, types 1, 2 and 6 covered 61.2%, 14.4% and 9.3% of the clones analyzed, respectively, while the remaining 14 only covered 21 clones, which accounted for 15.1% of the total. Twenty-four representative clones were sequenced and phylogenetically analyzed by referring to those currently available in RDP and GenBank databases. Although it was hard to assign these sequences to known species or genera due to the lack of the 18S rDNA sequence data of known marine free-living nematodes, the obtained sequences were assigned to the nematodes of Adenophorea. Among them, twelve sequences were close to Pontonema vulgate and Adoncholaimus sp., four to Daptonema procerus and two （identical） to Enoplus brews. Our results showed that free-living marine nematode diversities could be determined by PCR retrieving and analysis of the 18S rDNA sequences and an 18S rDNA sequence could be assigned to a species or a genus only if the 18S rDNA sequences of the free-living marine nematodes were accumulated to some extent.     

Molecular phylogenetic analysis of attached Ulvaceae species and free-floating Enteromorpha 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.     

Epiphytic bacterial communities on two common submerged macrophytes in Taihu Lake: diversity and host-specificity

Leaves of terrestrial and aquatic plants are home to a wide diversity of bacterial species. However, the diversity and variability of epiphytic bacteria on their submerged plant hosts remains poorly understood. We investigated the diversity and composition of epiphytic bacteria from two common submerged macrophytes: Vallisneria natans and Hydrilla verticillata in Taihu Lake, Jiangsu, China, using methods of terminal restriction fragment length polymorphisms (T-RFLP) and clone library analyses targeted at bacterial 16S rRNA genes. The results show that: (1) the libraries of the two waterweeds contain wide phylogenetic distribution of bacteria, and that the sequences of the two libraries can be separated into 93 OTUs (at 97% similar value); (2) Betaproteobacteria, including Burkholderiales, was the most abundant bacterial group on both plants. Cyanobacteria and Gammaproteobacteria were the second largest groups on V. natans and H. verticillata, respectively. Both clone libraries included some sequences related to those of methanotrophs and nitrogen-fixing bacteria; (3) Cluster analysis of the T-RFLP profiles showed two distinct clusters corresponding to the two plant populations. Both ANOSIM of the T-RFLP data and Libshuff analysis of the two clone libraries indicated a significant difference in epiphytic bacterial communities between the two plants. Therefore, the epiphytic bacterial communities on submerged macrophytes appear to be diverse and host-specific, which may aid in understanding the ecological functions of submerged macrophytes in general.     

Seasonal Distribution of Bioaerosols in the CoastalRegion of Qingdao

Bioaerosols were collected by using a six-stage bioaerosols sampler from September 2007 to August 2008 in the coastalregion of Qingdao, China. The terrestrial and marine microbes （including bacteria and fungi） were analyzed in order to understandthe distribution features of bioaerosols. The results show that the average monthly concentrations of terrestrial bacteria, marine bacte-ria, terrestrial fungi and marine fungi are in the ranges of 804515 CFUm-3, 91-468 CFUm-3, 76-647CFUm-3 and 231-1959CFUm-3,respectively. The concentrations of terrestrial bacteria, marine bacteria, terrestrial fungi, marine fungi and total microbes are thehighest in each microbial category during fall, high in spring, and the lowest in the summer and winter. The bacterial particles arecoarse in spring, autumn and winter. The sizes of fungal particle present the log-normal distribution in all the seasons.     

Effects of DNA extraction and universal primers on 16S rRNA gene-based DGGE analysis of a bacterial community from fish farming water

Among many reports investigating microbial diversity from environmental samples with denaturing gradient gel electrophoresis (DGGE), limited attention has been given to the effects of universal primers and DNA extraction on the outcome of DGGE analysis. In this study, these effects were tested with 16S rRNA gene-based DGGE on a bacterial community from farming water samples. The results indicate that the number of discernable bands in the DGGE fingerprint differed with the primer pairs used; the bands produced by 63f/518r, 341f/926r and 933f/1387r primer pairs were obviously fewer than those by 968f/1401r. Also, we found that each DNA extraction method resulted in different community profiles, reflected by the number and intensity of bands in the DGGE fingerprint. Furthermore, the main bands (theoretically representing dominant bacteria) differed with the extraction methods applied. It is therefore believed that the effects of universal primers and DNA extraction should be given more attention and carefully chosen before performing an investigation into a new environment with DGGE.     

Bacterial diversity, composition and temporal-spatial variation in the sediment of Jiaozhou Bay, China

Studies on the diversity and distribution of bacterial populations will improve the overall understanding of the global patterns of marine bacteria and help to comprehend local biochemical processes and environments. We evaluated the composition and the dynamics of bacterial communities in the sediment of Jiaozhou Bay (China) using PCR-denaturing gradient gel electrophoresis (DGGE). Sediment samples were collected from 10 different sites in May, August, and November 2008 and in February 2009. There was significant temporal variation in bacterial community composition at all sites. However, the spatial variation was very small. The DGGE analyses of bacterial communities were used to divide the 10 stations into three types. Canonical correspondence analysis (CCA) revealed that the changes in bacterial communities were driven by sediment properties. Sequence analysis of DGGE band-derived 16S rRNA gene fragments revealed that the dominant bacterial groups in the sediment were of the classes γ-proteobacteria and δ-proteobacteria and phyla Bacteroidetes and Nitrospirae. Our results provide considerable insight into the bacterial community structure in Jiaozhou Bay, China.     

Response of Microbial Community to Petroleum Stress and Phosphate Dosage in Sediments of Jiaozhou Bay,China

The dynamic microcosms were used to evaluate the effect of oil spills on microbial ecological system in marine sedi- ment and the enhancement of nutrient on the oil removal. The function and structure of microbial community caused by the oil pollu-tion and phosphate dosage were simultaneously monitored by dehydrogenase activity assay and PCR-denaturing gradient gel elec- trophoresis （DGGE） techniques. The results indicated that the amount of total bacteria in all dynamic microcosms declined rapidly with incubation time. The number of petroleum-degrading bacteria and the activity of sediment dehydrogenase were gradually en-hanced by petroleum in the oil-treated microcosms, while they both showed no obvious response to phosphate dosage. In comparison, phosphate spiked heterotrophic bacteria and they showed a significant increase in amount. DGGE profiles indicated that petroleum dosage greatly changed community structure, and the bacteria belonged to class Deltaproteobacteria, and phyla Bacteroidetes and Chlorobi were enriched. This study demonstrated that petroleum input greatly impacted the microbial community structure and con- sequently the marine sediment petroleum-degrading activity was enhanced. Phosphate dosage would multiply heterotrophic bacteria but not significantly enhance the petroleum degradation.     

Spatial distribution and controlling factors of sedimentary bodies in Jiaozhou Bay and Adjacent Sea Areas, Qingdao

The distributions of thickness of unconsolidated Quaternary sedimentary layers in Jiaozhou Bay and Qingdao offshore area were studied by using 1079-km high-resolution shallow seismic profiles and drilling core data, and the factors controlling the Quaternary evolution were discussed. The results show that such thickness distributions resulted from the coactions of geologic structures and marine hydrodynamic conditions since the Holocene. The geologic structures controlled the slope deposit, proluvial and fluvial fillings since the late Pleistocene. Holocene marine hydrodynamics eroded away sediments at the bay mouth, and tides carried these eroded materials to the sides of the bay mouth and released them there, forming channel-ridge-alternating geomorphic features. During transgressive processes, the sea level rose rapidly, and insufficient sediment supply and tidal actions yielded the relict sediments in the east of Qingdao offshore area.     

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.     

Genetic variation among white croaker populations

To investigate the genetic structures and differentiation of different wild populations of white croaker （Pennahia argentara）, horizontal starch gel electrophoresis was performed on 133 individuals collected from five different locations in China and Japan. The eleven enzyme systems revealed 15 loci, of which eleven were polymorphic. The percentage ofpolymorphic loci of white croaker populations varied from 6.67% to 53.3.3%; the mean observed and expected heterozygosity ranged from 0.0033 to 0.0133 and 0.0032 to 0.0191, respectively. The expected heterozygosity revealed a low genetic variability for white croaker in comparison with other marine fishes. The genetic distances between populations ranged from 0.00005 to 0.00026. A weak differentiation was observed within each clade and between clades; and no significant differences in gene frequencies among populations were observed in white croaker. Among the five populations, three Chinese populations showed more genetic diversity than that in Japanese populations.     

Nematode community structure and diversity pattern in sandy beaches of Qingdao,China

We investigated the diversity and structure of free-living marine nematode communities at three sandy beaches representing typical intertidal environments of a temperate zone in Qingdao,Shandong Province,China.Average nematode abundance ranged from 1006 to 2170 ind.10 cm-2,and a total of 34 nematode genera were recorded,of which only 8 were common in all the studied beaches.Pielou's evenness and Shannon-Wiener diversity index were the lowest at the second beach where nematode abundance was the highest.The highest species diversity index coincided with the lowest nematode abundance at Shilaoren beach.Sediment median grain size,sorting coefficient,and chlorophyll-a content were essential for differentiation in nematode abundance and species diversity,whereas taxonomic diversity of nematode was homogeneous across the three beaches.In 0–20 cm sediment profile,nematode abundance declined abruptly with depth,whereas nematode diversity changed gently with obvious difference in 16–20 cm layer.Sediment granulometry and chlorophyll-a content were the two foremost factors which influenced the vertical distribution pattern of nematode generic diversity.Non-selective deposit feeders constituted the most dominant trophic group,followed by epistratum feeders.Bathylaimus(family:Tripyloididae) dominated at the second and Yangkou beach,while Theristus(family:Xyalidae) prevailed at Shilaoren beach.Omnivores and predators became important at Shilaoren beach because of the high proportion of Enoplolaimus.Even though,nematode community of the studied beaches did not differ significantly from each other.     

Molecular phylogenetic analysis of dinoflagellate Scrippsiella trochoidea isolated from the East Asian waters

Previous studies found intraspecific diversity in Scrippsiella trochoidea A. R. Loeblich III, a widely distributed calcareous cyst-producing dinoflagellate. In this study, three strains (ST-1, ST-D6 and ST-K) of S. trochoidea isolated from the East Asian waters were studied, together with other geographical strains, to resolve their phylogenetic relationships. For the three East Asian isolates, two highly diverse regions of nuclear-encoded ribosomal DNA (rDNA), the 5.8S rDNA and its flanking internal transcribed spacers 1 and 2, and the 5' portion of the large-subunit rDNA (encompassing the "D1" and "D2" domains) were sequenced. Homologous sequences from other geographical isolates were selected from the GenBank database and the phylogenetic relationships were inferred from the molecular data of these strains. Strains of S. trochoidea were found to cluster into three major clades (STR1, STR2 and STR3), as reported in previous studies. Two of the three strains ST-1 and ST-K, were grouped in clade STR2, the other strain, ST-D6, belonged to clade STR3. The intraspecific diversity of S. trochoidea in East Asian waters makes it necessary to carry out phylogenetic investigations in combination with data of biogeography, population dynamics, and life cycle on the ecophysiology of a region.     

Distribution of Protists in the Deep South China Sea Revealed by High-Throughput Sequencing

Protists(microbial eukaryotes)are indispensable members of the marine microbial food web.In recent years,organisms living in the deep sea(>1000 m water depth)have increasingly become the focus of research;however,studies on protistan assemblages are relatively scarce compared with their prokaryotic counterparts.In the present study,high-throughput sequencing of the hypervariable V9 region of the 18S rRNA gene was used to explore the community composition of protists in bathypelagic waters of the South China Sea.Based on the analysis of the alpha and beta diversities of 14 samples,we discovered:1、members belonging to Rhizaria,Alveolata,and Excavata were the dominant groups in terms of both relative sequence abundance and operational taxonomic unit(OTU)richness in all samples,although their relative contributions differed among different samples;2、cluster analysis showed that the distribution of protistan assemblages was related neither to the sampling location nor to the water depth,and other environmental factors might have caused the differences among the communities;3、phototrophs,including members of the Bacillariophyta,Bolidophyceae,Dictyochophyceae,Prasinophyceae,and Prymnesiophyceae,were detected in all samples,which indicated their contributions to the downward transportation via the biological pump and the potential presence of phagotrophy of these phototrophic cells in the deep ocean.     

Did Species and Functional Diversities of Sandy Intertidal Marine Nematodes Reveal Similar Response to Environmental Changes?

Free living marine nematodes were sampled from two sandy beaches in Dalian City, in December of 2015, and April, July,and October of 2016. The spatial and seasonal variations of marine nematode species diversity(based on species abundance dataset)and functional diversity(based on functional traits dataset: feeding types and life history strategies) were investigated to understand the environmental drivers and how they respond to specific environmental variations. Sediment granularity was reveale...     

INTRODUCTION, SPAT REARING AND EXPERIMENTAL CULTURE OF BAY SCALLOP, ARGOPECTEN IRRADIANS LAMARCK

Bay scallops were introduced from the east coast of the U.S. into China to shorten the economic turn-over from 2 to 1 year. Parent scallops were carried to Qingdao on Dec. 20. 1982 and stocked in indoor tanks at controlled temperature and fed with a mixture of Phaeodictylum tricomutum, Pyrarnmonas sp. and Chhrella sp. They spawned on Jan. 26 of the next year. The larvae were reared at a temperature of 18 -21℃ and fed with Isochrysis galbana, Pyramimonas sp. and Chorella sp. In 4 weeks' growing, the spats averaged 827um. They attained a height of 6.9 mm on May 9. In the middle of May, the seed scallops were transferred to Luoyuan Bay in Fujian Province, and Jiaozhou Bay, as well as the area off Taiping Jiao Cape, Qingdao, Shandong Province for experimental culture in plastic netcages suspended on a single line raft.Bay scallops cultured in . Luoyuan Bay grew to an averaged shell height of 10.4 mm. In Jiaozhou Bay and the Taiping Jiao Cape culture area, they grew to SO mm in average shell height (marketa     

Phytoplankton diversity in the East China Sea and Yellow Sea measured by PCR-DGGE and its relationships with environmental factors

Relationships between phytoplankton community composition and environmental variables in the East China Sea (ECS) and Yellow Sea (YS) were investigated using geochemical and molecular microbiology methods. The diversity of phytoplankton was characterized using cultivation-independent PCR-based denaturing gradient gel electrophoresis (DGGE). Groups resulting from unweighted pair-group method with arithmetic averages clustering of the DGGE profiles showed good consistency with the eco-environmental characteristics of the sea area they belonged to. Additionally, the clustering results based on DGGE fingerprinting and those based on morphological compositions were practically identical. The relationship of phytoplankton diversity to environmental factors was statistically analyzed. Temperature, dissolved inorganic nitrogen (DIN), and silicate-Si were found significantly related to the phytoplankton community composition. Canonical correspondence analysis (CCA) was performed to reveal the relationship between community composition and these three environmental factors. Generally, values of the ECS are clearly separated from those of the YS in the CCA biplot, due to mainly the effect of temperature and DIN.     

Comparison of intestinal bacterial communities in grass carp, Ctenopharyngodon idellus, from two different habitats

The intestinal bacteria of vertebrates form a close relationship with their host.External and internal conditions of the host,including its habitat,affect the intestinal bacterial community.Similarly,the intestinal bacterial community can,in turn,influence the host,particularly with respect to disease resistance.We compared the intestinal bacterial communities of grass carp that were collected from farm-ponds or a lake.We conducted denaturing gradient gel electrophoresis of amplified 16S rRNA genes,from which 66 different operational taxonomic units were identified.Using both the unweighted pair-group method with arithmetic means clustering and principal component analysis ordination,we found that the intestinal bacterial communities from the two groups of pond fish were clustered together and inset into the clusters of wild fish,except for DF-7,and there was no significant correlation between genetic diversity of grass carp and their intestinal bacterial communities(Mantel one-tailed test,R=0.157,P=0.175).Cetobacterium appeared more frequently in the intestine of grass carp collected from pond.A more thorough understanding of the role played by intestinal microbiota on fish health would be of considerable benefit to the aquaculture industry.     

Molecular detection of microbial communities associated with Microcystis vs Synechococcus dominated waters in Tianjin,China

Harmful cyanobacterial blooms cause many ecological disasters worldwide. During the development of cyanobacterial blooms, the diversity and domination of cyanobacterial taxa are of a particular concern. In this study, the microbial community structure within a water system, such as in Yuqiao Reservoir and Haihe River in Tianjin City, China, was compared by using next-generation sequencing. A total of 5 001 operational taxonomic units were obtained and clustered from filtered 16 S rDNA V3–V4 region sequences. The cyanobacterial and microbial structures greatly differed in these two water areas. Microcystis was dominant in Yuqiao, whereas Synechococcus was dominant in Haihe. Proteobacteria species were dominant among all detected samples. The relative abundances of Bacteroidetes and Planctomycetes were higher in Yuqiao Reservoir than in Haihe River, whereas Firmicutes and Verrucomicrobia were relatively abundant in Haihe River. Further analyses indicated that the domination of both cyanobacteria was strongly related to several environmental factors, such as total nitrogen, total phosphorus, and dissolved oxygen, reflecting the role of trophic states in shaping the dominance of cyanobacterial taxa. The present study provided the example for Microcystis and Synechococcus dominance along a cyanobacterial bloom in north China. Applying highthroughput sequencing could offer a wide field of vision in analyzing microbial community structures.