The complete mitochondrial genomes of Asio flammeus and Asio otus were se- quenced and found to span 18858 bp and 18493 bp, respectively. It is surprising to find the for- mer to be the largest among all avian mitocho...The complete mitochondrial genomes of Asio flammeus and Asio otus were se- quenced and found to span 18858 bp and 18493 bp, respectively. It is surprising to find the for- mer to be the largest among all avian mitochondrial genomes sequenced so far. The two ge- nomes have very similar gene order with that of Gallus gallus, neither contains the pseudo con- trol region, but both have a single extra base, namely Cytidine, at position 174 in ND3 gene. The control regions of Asio flammeus and Asio otus’ mitochondrial genomes span 3288 bp and 2926 bp respectively, which are the longest among vertebrates except for Myxine glutinosa and con- tribute to the large size of two genomes. The 3′end of the control region of Asio flammeus and Asio otus contains many tandemly repeated sequences, which are highly similar to a putative control element, i.e. Mt5, and may form stable stem-loop secondary structures. Such repeated sequences probably play an important role in regulating transcription and replication of mito- chondrial genome. Our results may provide important clues for uncovering the origin and evolu- tion mechanisms of mitochondrion genome.展开更多
Mining relationships between microbes and the environment they live in are crucial to understand the intrinsic mechanisms that govern cycles of carbon, nitrogen and energy in a microbial community. Building upon next-...Mining relationships between microbes and the environment they live in are crucial to understand the intrinsic mechanisms that govern cycles of carbon, nitrogen and energy in a microbial community. Building upon next- generation sequencing technology, the selective capture of 16S rRNA genes has enabled the study of co-occurrence patterns of microbial species from the viewpoint of complex networks, yielding successful descriptions of phenomena exhibited in a microbial community. However, since the effects of such environmental factors as temperature or soil conditions on microbes are complex, reliance on the analysis of co-occurrence networks alone cannot elucidate such complicated effects underlying microbial communities. In this study, we apply a statistical method, which is called Boolean implications for metagenomic studies （BIMS） for extracting Boolean implications （IF-THEN relationships） to capture the effects of environmental factors on microbial species based on 16S rRNA sequencing data. We first demonstrate the power and effectiveness of BIMS through comprehensive simulation studies and then apply it to a 16S rRNA sequencing dataset of real marine microbes. Based on a total of 6,514 pairwise relationships identified at a low false discovery rate （FDR） of 0.01, we construct a Boolean implication network between operational taxonomic units （OTUs） and environmental factors. Relationships in this network are supported by literature, and, most importantly, they bring biological insights into the effects of environmental factors on microbes. We next apply BIMS to detect three-way relationships and show the possibility of using this strategy to explain more complex relationships within a microbial community.展开更多
Although the taxonomy of oligotrich ciliates has been widely investigated,yet the species diversity remains poorly known.We newly designed a pair of oligotrich-specific LSU rDNA primers covering the 600-bp D1/D2 regio...Although the taxonomy of oligotrich ciliates has been widely investigated,yet the species diversity remains poorly known.We newly designed a pair of oligotrich-specific LSU rDNA primers covering the 600-bp D1/D2 region,and it was effective for detecting oligotrich species.Using the primers,we constructed the cloning libraries to investigate the species diversity of oligotrichs in the northern coastal waters of the South China Sea.In total,165 oligotrich sequences were obtained from five widely separated sampling sites.Sixty operational taxonomic units(OTUs)were obtained at 99%similarity threshold,and low-abundance OTUs with no more than two sequences contributed most of these(about 78%).Our findings are consistent with previous morphological studies,Strombidium was found the most abundant and widely distributed genus in this area.In addition,the BLAST search in the NCBI database resulted in 95%OTUs matching with named oligotrich species in similarity below 99%.Therefore,oligotrich morphospecies diversity has been underestimated as low-abundance species,and the LSU rDNA oligotrich sequence database needs to be better promoted.展开更多
Eighteen agar media were tested for the culture of gut-associated bacteria from farmed adult turbot （Scophthalmus maximus）, including 16 agar media with or without 1% gastrointestinal （GI） supernatant, or with 2% ...Eighteen agar media were tested for the culture of gut-associated bacteria from farmed adult turbot （Scophthalmus maximus）, including 16 agar media with or without 1% gastrointestinal （GI） supernatant, or with 2% or 4% GI supernatant. A total of 1 711 colonies were analyzed and 24 operational taxonomic units （OTUs） were identified. The greatest bacterial diversity was isolated on Zobell 2216E/ Zobell 2216E＋ agar media, whereas MRS/MRS＋ agar media produced a low diversity of colonies, Agar media with GI supernatant （1%, 2%, or 4%） showed increased diversity and yielded different profiles of OTUs from the corresponding original media, suggesting that GI supernatant provides substances that enhance the culture efficiency of bacteria from the turbot GI tract. The large majority of the colonies （82%） were 7-Proteobacteria, whereas 15.6% and 2.4% of colonies were Firmicutes and Actinobacteria, respectively. At the genus level, 49.4% of all colonies were assigned to Vibrio. Other potential pathogens, including Pseudomonas, Photobacterium, and Enterobacter, and potential probiotics, including Bacillus, Paenibacillus, and Pseudomonas, were also isolated on agar media. Most cultured bacteria belonged to species that were first described in the turbot GI tract. The impact of these species on turbot physiology and health should be investigated further.展开更多
This study explores the diversity and structure of prokaryotic communities (Archaea and Bacteria) of 2 tropical volcanic lakes (Nyos and Monoun) in Cameroon, using 16SrRNA sequences. Metagenomics analysis of sequences...This study explores the diversity and structure of prokaryotic communities (Archaea and Bacteria) of 2 tropical volcanic lakes (Nyos and Monoun) in Cameroon, using 16SrRNA sequences. Metagenomics analysis of sequences showed that most OTUs (Operational Taxonomic Units) were associated with 26 phyla (23 for Bacteria and 3 for Archaea) in Nyos and 36 phyla (33 for Bacteria and 3 for Archaea) in Monoun. In both lakes, Proteobacteria for Bacteria and Crenarchaea for Archaea were predominant and present at all depths but in different proportions. Bacterial community compositions were generally dominated by members of Proteobacteria, Firmicutes, Actinobacteria, Chloroflexi and Bacteroidetes covering about 98% of the sequences. Crenarchaea, Thaumarchaea and Euryarchaea were the three main phyla of Archaea common to both lakes. The amount of virus and total bacteria was determined by flow cytometry technic and the evaluated ratio ranged from 0.2 to 1.2 at Nyos and from 0.6 to 2.6 at Monoun. For both lakes, the correlation was very significant between viruses and total bacteria. The depth-dependent variability is discussed with chemical and physical environmental parameters. These could significantly influence virus-mediated bacterial lysis and abundance and vertical stratification of the prokaryotic community.展开更多
基金This work was supported by the National Natural Science Foundation of China(Grant No.30170505).
文摘The complete mitochondrial genomes of Asio flammeus and Asio otus were se- quenced and found to span 18858 bp and 18493 bp, respectively. It is surprising to find the for- mer to be the largest among all avian mitochondrial genomes sequenced so far. The two ge- nomes have very similar gene order with that of Gallus gallus, neither contains the pseudo con- trol region, but both have a single extra base, namely Cytidine, at position 174 in ND3 gene. The control regions of Asio flammeus and Asio otus’ mitochondrial genomes span 3288 bp and 2926 bp respectively, which are the longest among vertebrates except for Myxine glutinosa and con- tribute to the large size of two genomes. The 3′end of the control region of Asio flammeus and Asio otus contains many tandemly repeated sequences, which are highly similar to a putative control element, i.e. Mt5, and may form stable stem-loop secondary structures. Such repeated sequences probably play an important role in regulating transcription and replication of mito- chondrial genome. Our results may provide important clues for uncovering the origin and evolu- tion mechanisms of mitochondrion genome.
文摘Mining relationships between microbes and the environment they live in are crucial to understand the intrinsic mechanisms that govern cycles of carbon, nitrogen and energy in a microbial community. Building upon next- generation sequencing technology, the selective capture of 16S rRNA genes has enabled the study of co-occurrence patterns of microbial species from the viewpoint of complex networks, yielding successful descriptions of phenomena exhibited in a microbial community. However, since the effects of such environmental factors as temperature or soil conditions on microbes are complex, reliance on the analysis of co-occurrence networks alone cannot elucidate such complicated effects underlying microbial communities. In this study, we apply a statistical method, which is called Boolean implications for metagenomic studies （BIMS） for extracting Boolean implications （IF-THEN relationships） to capture the effects of environmental factors on microbial species based on 16S rRNA sequencing data. We first demonstrate the power and effectiveness of BIMS through comprehensive simulation studies and then apply it to a 16S rRNA sequencing dataset of real marine microbes. Based on a total of 6,514 pairwise relationships identified at a low false discovery rate （FDR） of 0.01, we construct a Boolean implication network between operational taxonomic units （OTUs） and environmental factors. Relationships in this network are supported by literature, and, most importantly, they bring biological insights into the effects of environmental factors on microbes. We next apply BIMS to detect three-way relationships and show the possibility of using this strategy to explain more complex relationships within a microbial community.
基金Supported by the National Natural Science Foundation of China(Nos.31772440,31430077,41576124,31761133001)the Pearl River Science and Technology Nova Program of Guangzhou(No.201610010162) to YZ+1 种基金Guangdong MEPP Fund(No.GDOE(2019)A23)the Special Support Program of Guangdong Province to YZ
文摘Although the taxonomy of oligotrich ciliates has been widely investigated,yet the species diversity remains poorly known.We newly designed a pair of oligotrich-specific LSU rDNA primers covering the 600-bp D1/D2 region,and it was effective for detecting oligotrich species.Using the primers,we constructed the cloning libraries to investigate the species diversity of oligotrichs in the northern coastal waters of the South China Sea.In total,165 oligotrich sequences were obtained from five widely separated sampling sites.Sixty operational taxonomic units(OTUs)were obtained at 99%similarity threshold,and low-abundance OTUs with no more than two sequences contributed most of these(about 78%).Our findings are consistent with previous morphological studies,Strombidium was found the most abundant and widely distributed genus in this area.In addition,the BLAST search in the NCBI database resulted in 95%OTUs matching with named oligotrich species in similarity below 99%.Therefore,oligotrich morphospecies diversity has been underestimated as low-abundance species,and the LSU rDNA oligotrich sequence database needs to be better promoted.
基金Supported by the National High Technology Research and Development Program of China(863 Program)(No.2007AA09Z444)
文摘Eighteen agar media were tested for the culture of gut-associated bacteria from farmed adult turbot （Scophthalmus maximus）, including 16 agar media with or without 1% gastrointestinal （GI） supernatant, or with 2% or 4% GI supernatant. A total of 1 711 colonies were analyzed and 24 operational taxonomic units （OTUs） were identified. The greatest bacterial diversity was isolated on Zobell 2216E/ Zobell 2216E＋ agar media, whereas MRS/MRS＋ agar media produced a low diversity of colonies, Agar media with GI supernatant （1%, 2%, or 4%） showed increased diversity and yielded different profiles of OTUs from the corresponding original media, suggesting that GI supernatant provides substances that enhance the culture efficiency of bacteria from the turbot GI tract. The large majority of the colonies （82%） were 7-Proteobacteria, whereas 15.6% and 2.4% of colonies were Firmicutes and Actinobacteria, respectively. At the genus level, 49.4% of all colonies were assigned to Vibrio. Other potential pathogens, including Pseudomonas, Photobacterium, and Enterobacter, and potential probiotics, including Bacillus, Paenibacillus, and Pseudomonas, were also isolated on agar media. Most cultured bacteria belonged to species that were first described in the turbot GI tract. The impact of these species on turbot physiology and health should be investigated further.
文摘This study explores the diversity and structure of prokaryotic communities (Archaea and Bacteria) of 2 tropical volcanic lakes (Nyos and Monoun) in Cameroon, using 16SrRNA sequences. Metagenomics analysis of sequences showed that most OTUs (Operational Taxonomic Units) were associated with 26 phyla (23 for Bacteria and 3 for Archaea) in Nyos and 36 phyla (33 for Bacteria and 3 for Archaea) in Monoun. In both lakes, Proteobacteria for Bacteria and Crenarchaea for Archaea were predominant and present at all depths but in different proportions. Bacterial community compositions were generally dominated by members of Proteobacteria, Firmicutes, Actinobacteria, Chloroflexi and Bacteroidetes covering about 98% of the sequences. Crenarchaea, Thaumarchaea and Euryarchaea were the three main phyla of Archaea common to both lakes. The amount of virus and total bacteria was determined by flow cytometry technic and the evaluated ratio ranged from 0.2 to 1.2 at Nyos and from 0.6 to 2.6 at Monoun. For both lakes, the correlation was very significant between viruses and total bacteria. The depth-dependent variability is discussed with chemical and physical environmental parameters. These could significantly influence virus-mediated bacterial lysis and abundance and vertical stratification of the prokaryotic community.
