Yonghui Zeng

Bacterial Diversity of Freshwater Alpine Lake Puma Yumco on the Tibetan Plateau

Bacterial community in the water of Lake Puma Yumco, a freshwater alpine lake on the Tibetan Plateau was studied for the first time using an integrated approach including water chemistry and culture-dependent and -independent methods. Microbial abundance in the lake water was from 1.59 × 105 to 3.37 × 105 cells mL− 1, and bacteria were evenly distributed in the lake due to its uniform water physical-chemistry. Obtained isolates were affiliated with α-, β- and γ-Proteobacteria, Actinobacteria and Bacteroidetes, among which γ-Proteobacteria isolates were dominant. Retrieved bacterial 16S rRNA gene clones fell into α-, β- and γ-Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Planctomycetes, Verrucomicrobia and Chloroflexi. Bacterial diversity in Lake Puma Yumco was higher than that in other Tibetan lakes at levels of both phyla and clusters. A half of total clones in Lake Puma Yumco were members of the widespread typical freshwater bacterial clusters. The low temperature of Lake Puma Yumco also made it possess unique freshwater bacteria members.

Bacteria variabilities in a Tibetan ice core and their relations with climate change

Ministry of Science and Technology of the Peoples Republic of China [2005CB422004]; National Natural Science Foundation of China [40121101, 40401054]; Innovation Program [KZCX3-SW-339]; Chinese Academy of Sciences

Bacterial Community of the Largest Oligosaline Lake, Namco on the Tibetan Plateau

Bacterial abundances and diversity in the surface water of Lake Namco, the largest oligosaline lake on the Tibetan Plateau, were examined using flow cytometry approach and constructing 16S rRNA gene clone libraries. Bacterial abundances were from 0.08 × 106 to 1.6 × 106 cells mL−1, and were in the reported range of other lakes of the Tibetan Plateau and high mountain regions. Bacterial abundances were significantly correlated with the concentrations of chlorophyll a (chl a), but showed no significant relationship with the dissolved organic carbon (DOC), which suggested that the amount of DOC released by algae was the key factor determining the bacterial abundance rather than the total DOC. The total trace elements concentrations also obviously connected with bacterial abundances, and 9 of 20 elements showed significant relationship. Bacterial 16S rRNA gene clone sequences were affiliated to the α-, β-, γ-, δ-, and ϵ-Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, Acidobacteria, Planctomycetes, Verrucomicrobia, Candidate division OD1, or unclassified, and among these the β-Proteobacteria dominated. Bacteria in Lake Namco were most closely related to those retrieved from freshwater habitats. Relatively few sequences were closely related to those recovered from saline habitats. Eleven of 34 typical freshwater bacterial clusters were detected in the oligosaline Lake Namco. Bacterial diversity within the lake varied and was connected with the concentrations of DOC and chl a.

Natural community structure of cyanobacteria in the South China Sea as revealed by rpoC1 gene sequence analysis

Aims:  To examine the community structure of cyanobacterial populations of the South China Sea on the surface and at depth of 80 m.

Genetic diversity assessment of anoxygenic photosynthetic bacteria by distance‐based grouping analysis of pufM sequences

Aim:  To assess how completely the diversity of anoxygenic phototrophic bacteria (APB) was sampled in natural environments.

Vertical distribution and phylogenetic composition of bacteria in the Eastern Tropical North Pacific Ocean

The vertical community structure of bacteria along a depth profile in the Eastern Tropical North Pacific Ocean (13 degrees N, 104 degrees W) was studied by flow cytometry measurement and 16S rRNA gene clone libraries analysis. Picoeukaryotes and Synechococcus peaked at 30 m and decreased sharply below 50 m, while Prochlorococcus peaked at both 30 and 100 m layers and disappeared below 200 m. Heterotrophic bacteria peaked above shallow thermocline and decreased along the depth profile. Sequences of total 322 clones from four clone libraries (10, 100, 1000, and 3000 m) clustered into nine major lineages. gamma-Proteobacteria dominated all the depths and occupied almost the whole bacterial community at the 3000 m. alpha-Proteobacteria was abundant throughout the water column except near the sea bottom, and delta-Proteobacteria peaked at the 1000 m depth. Cyanobacteria were primarily limited to the photic zone, and the genetic diversity of Prochlorococcus showed a good correlation with niche adaptation. The appearance of the Cytophaga-Flexibacter-Bacteroides (CFB) group did not show a clear relationship with depth. Actinobacteria were found both in the photic zone and in deep water. Planctomyetes, Acidobacteria, and Verrucomicrobia were present as minor groups and more dominant in the deeper layers of water.

Comparison of bacterioplankton communities in three mariculture ponds farming different commercial animals in subtropical Chinese coast

In order to explore the responses of the bacterioplankton community to different types of aquaculture environments, three mariculture ponds comprised of groupers (Epinephelus diacanthus, ED), prawns (Penaeus vannamei, PV), and abalone (Haliotisdiversicolor supertexta, HDS) in southeast, coastal China were investigated. The free-living bacterial diversity was analyzed through the construction of 16S rDNA clone library. A total of 203 16S rDNA sequences from three clone libraries were classified into 118 operational taxonomic units (OTUs), of which 51, 31, and 42 OTUs were distributed in the ED, PV, and HDS pond, respectively, with Bacteroidetes (30.6%), Actinobacteria (55.2%), and Cyanobacteria (32.8%) as the dominant division in the respective ponds. Meanwhile, each pond occupied some unique OTUs that were affiliated with uncommon (sub-)phyla, such as candidate OP11 division, Acidobacteria, Deltaproteobacteria, Planctomycetes, and Verrucomicrobia. Bacterial diversity in the ED pond was the richest, followed by the HDS and the PV pond. OTUs of 61.9% and 94.9% have less than 90% and 97% similarity to their nearest neighbors in public databases, respectively. All OTUs were grouped into 67 clusters, covering 11 (sub-)phyla. The OTUs only from single pond distributed in 53 clusters (79.1%), the OTUs shared by two ponds were affiliated with 14 clusters (20.9%), and none of clusters was formed by the OTUs which commonly originated from the three pond libraries, suggesting that the composition of bacterial populations in these ponds were significantly different. These results indicate that the aquatic environment created by different mariculture animals may foster very special and complex bacterial communities.

Long PCR-RFLP of 16S-ITS-23S rRNA genes: a high-resolution molecular tool for bacterial genotyping

To perform a systematic evaluation of the applicability, validity and reliability of the long PCR‐RFLP of 16S‐ITS‐23S rRNA genes for bacterial genotyping using both sequences retrieved from public genome databases and the experimental data obtained on bacterial cultures.

Whole-Genome Sequences of an Aerobic Anoxygenic Phototroph, Blastomonas sp. Strain AAP53, Isolated from a Freshwater Desert Lake in Inner Mongolia, China

ABSTRACT Blastomonas is a strictly aerobic bacteriochlorophyll a-producing genus within the alpha-4 Proteobacteria. Here we report the first genome sequence from this genus. The draft genome of Blastomonas sp. strain AAP53 contains a split photosynthesis gene cluster and two gene clusters encoding a flagellar system. Genes for the autotrophic CO2 fixation pathway are absent.

Whole-genome sequence of a freshwater aerobic anoxygenic phototroph, Porphyrobacter sp. strain AAP82, isolated from the Huguangyan Maar Lake in Southern China.

ABSTRACT The Porphyrobacter genus (of the class Alphaproteobacteria) contains aerobic anoxygenic phototrophic species. Here we report a draft genome sequence of a freshwater bacterium, Porphyrobacter sp. strain AAP82. It contains a 38-kb-long photosynthesis gene cluster, but carbon-fixation genes are absent. The presence of respiratory enzymes, tricarboxylic acid (TCA) cycle, and the Entner-Doudoroff pathway demonstrates its aerobic photoorganotrophic character.