Gaosen Zhang

Bacterial diversity in the foreland of the Tianshan No. 1 glacier, China

There is compelling evidence that glaciers are retreating in many mountainous areas of the world due to global warming. With this glacier retreat, new habitats are being exposed that are colonized by microorganisms whose diversity and function are less well studied. Here, we characterized bacterial diversity along the chronosequences of the glacier No. 1 foreland that follows glacier retreat. An average of 10 000 sequences was obtained from each sample by 454 pyrosequencing. Using non-parametric and rarefaction estimated analysis, we found bacterial phylotype richness was high. The bacterial species turnover rate was especially high between sites exposed for 6 and 10 yr. Pyrosequencing showed tremendous bacterial diversity, among which the Acidobacteria, Actinobacteria, Bacteroidetes and Proteobacteria were found to be present at larger numbers at the study area. Meanwhile, the proportion of Bacteroidetes and Proteobacteria decreased and the proportion of Acidobacteria increased along the chronosequences. Some known functional bacterial genera were also detected and the sulfur- and sulfate-reducing bacteria were present in a lower proportion of sequences. These findings suggest that high-throughput pyrosequencing can comprehensively detect bacteria in the foreland, including rare groups, and give a deeper understanding of the bacterial community structure and variation along the chronosequences.

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. Phylogenetic analysis of the sequenced DGGE bands revealed a great diversity of bacteria. The Proteobacteria, consisting of the alpha, beta, and gamma subdivisions, 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 gamma-Proteobacteria correlated with a significant increase in polyphenol oxidase in the rhizosphere soil of A. 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.

Pyrosequencing Reveals Bacterial Diversity in the Rhizosphere of Three Phragmites australis Ecotypes

Here we present the use of high-throughput DNA pyrosequencing to assess bacterial diversity in the rhizosphere of three Phragmites australis ecotypes from the Hexi Corridor, China. In total, 43404 sequences were obtained for the three ecotypes, representing 31 phyla and a small amount of unclassified bacteria. The predominant bacterial groups in the rhizosphere of P. australis were Proteobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes and Planctomycetes. The bacterial community structure varied with the different degrees of wetland degradation, which were exhibited by the three P. australis ecotypes in the study area. At the phylum level, the Caldiserica, Chlamydiae, Deferribacteres, Lentisphaerae, and candidate division WS3 were only detected in the swamp reed (SR) sample. Then, δ-proteobacteria, Acidobacteria, Cyanobacteria and Fusobacteria decreased, the Actinobacteria increased with the degree of degradation from SR through salt meadow reed (SMR) to dune reed (DR). The functional bacterial genera also varied with wetland degradation. The sulfur and sulfate-reducing, nitrifying and nitrogen-fixing bacteria were more abundant in the rhizosphere of the SR sample. Methane-oxidizing bacteria were abundant in the SR and DR samples but less so in the SMR. In our study, pyrosequencing of different P. australis ecotypes provided insight into the structural variation of the rhizosphere bacterial community. This study gave a database for the use of bacteria in the protection and ecological restoration of wetland.

Tag-encoded pyrosequencing analysis of bacterial diversity within different alpine grassland ecosystems of the Qinghai-Tibet Plateau, China

The Qinghai-Tibet Plateau is sensitive to climate change, with ecosystems that are important with respect to scientific research. Here high-throughput DNA pyrosequencing was used to assess bacterial diversity within different alpine grassland ecosystems of the Qinghai-Tibet Plateau, China. In total, 34,759 sequences were obtained for the three ecosystems––alpine cold swamp meadow (ASM), alpine cold meadow (AM), alpine sandy grassland (ASG), and 31 phyla and a small number of unclassified bacteria were detected. The bacterial community structures were different for each alpine grassland ecosystem. The Proteobacteria and Acidobacteria were the predominant phyla in all three ecosystems. Besides this, Actinobacteria and Chloroflexi were abundant in ASM, Bacteroidetes, Gemmatimonadetes and Verrucomicrobia were abundant in AM, and Actinobacteria were abundant in ASG. In addition, the functional bacterial genera also differed with each alpine grassland ecosystem. The ASM contained more nitrifying bacteria, methane-oxidizing bacteria and sulfur- and sulfate-reducing bacteria, whereas the ASG ecosystem contained more nitrogen-fixing bacteria. Pyrosequencing provided a greater insight into bacterial diversity within different alpine grassland ecosystems than previously possible, and gave key data for the involvement of bacteria in the protection of alpine grassland ecosystems of the Qinghai-Tibet Plateau, China.

The diversity and biogeography of the communities of Actinobacteria in the forelands of glaciers at a continental scale

Glacier forelands, where the initially exposed area is unvegetated with minimal human influence, are an ideal place for research on the distributions and biogeography of microbial communities. Actinobacteria produce many bioactive substances and have important roles in soil development and biogeochemical cycling. However, little is known about the distribution and biogeography of Actinobacteria in glacier forelands. Therefore, we investigated the patterns of diversity and the biogeography of actinobacterial communities of the inhabited forefields of 5 glaciers in China. Of the bacteria, the mean relative abundance of Actinobacteria was 13.1%, and 6 classes were identified in the phylum Actinobacteria. The dominant class was Actinobacteria (57%), which was followed in abundance by Acidimicrobiia (19%) and Thermoleophilia (19%). When combined, the relative abundance of the other three classes, the MB-A2-108, Nitriliruptoria and Rubrobacteria, was only 2.4%. Abiogeographic pattern in the forelands of the 5 glaciers in China was not detected for actinobacterial communities. Compared with 7 other actinobacterial communities found in the forelands of glaciers globally, those in the Southern Hemisphere were significantly different from those in the Northern Hemisphere. Moreover, the communities were significantly different on the separate continents of the Northern Hemisphere. The dissimilarity of the actinobacterial communities increased with geographic distance (r=0.428, p=0.0003). Because of environmental factors, the effect of geography was clear when the distance exceeded a certain continent-level threshold. With the analysis of indicator species, we found that each genus had a geographic characteristic, which could explain why the communities with greater diversity were more strongly affected by biogeography.

Microbial diversity in the saline-alkali soil of a coastal Tamarix chinensis woodland at Bohai Bay, China

Soil salinization or alkalization is a form of soil desertification. Coastal saline-alkali soil represents a type of desert and a key system in the network of ecosystems at the continent-ocean interface. Tamarix chinensis is a drought-tolerant plant that is widely distributed in the coastal saline-alkali soil of Bohai Bay, China. In this study, we used 454 pyrosequencing techniques to investigate the characteristics and distribution of the microbial diversity in coastal saline-alkali soil of the T. chinensis woodland at Bohai Bay. A total of 20,315 sequences were obtained, representing 19 known bacterial phyla and a large proportion of unclassified bacteria at the phylum level. Proteobacteria, Acidobacteria and Actinobacteria were the predominant phyla. The coverage of T. chinensis affected the microbial composition. At the phylum level, the relative abundance of γ-Proteobacteria and Bacteroidetes decreased whereas Actinobacteria increased with the increasing coverage of T. chinensis. At the genus level, the proportions of Steroidobacter, Lechevalieria, Gp3 and Gp4 decreased with the increase of the vegetation coverage whereas the proportion of Nocardioides increased. A cluster analysis showed that the existing T. chinensis changed the niches for the microorganisms in the coastal saline-alkali soil, which caused changes in the microbial community. The analysis also distinguished the microbial community structure of the marginal area from those of the dense area and sparse area. Furthermore, the results also indicated that the distance to the seashore line could also affect certain groups of soil bacteria in this coastal saline-alkali soil, such as the family Cryomorphaceae and class Flavobacteria, whose population decreased as the distance increased. In addition, the seawater and temperature could be the driving factors that affected the changes.

Diversity and Succession of Actinobacteria in the Forelands of the Tianshan Glacier, China

ABSTRACT Actinobacteria are typically soil bacteria that have important roles in soil development and biogeochemical cycling. However, little is known about the occurrence or the succession of communities of Actinobacteria in new habitats. In this study, we investigated the diversity and succession of the actinobacterial communities that inhabited the forelands of the Tianshan Glacier (China), which ranged in successional age from 0 to 100 years since the forefield was deglaciated. Actinobacteria was one of the dominant phyla in the glacier foreland and included the orders Acidimicrobiales, Actinomycetales, Rubrobacteriales and Solirubrobacteriales. Actinomycetales was the dominant order, but its relative abundance decreased through the chronosequence. Acidimicrobiales and Solirubrobacteriales were more abundant in the late stages of succession than in the early ones. The abundance of Rubrobacteriales was only high at 74a. The dominant genera Nocardioides and Arthrobacter were widely distributed and were found in each stage of succession. With nonparametric and rarefaction estimated analyses, we found that the phylotype richness of Actinobacteria was significantly correlated with time (r = 0.886, p = 0.019). The succession of actinobacterial communities was divided into 3 stages: the early stage (6a), the intermediate stage (10a and 20a) and the late stage (60a, 74a, and 100a). Based on the canonical correspondence analysis, the actinobacterial communities were affected significantly by soil pH (r = −0.834, p = 0.039) and somewhat by the C/N ratio (r = 0.783, p = 0.066). The nonmetric multidimensional scaling analysis showed that the effect of geographical isolation on the actinobacterial communities was greater than that of the soils in the development of the chronosequence.

Diversity of Bacterial Communities in the Snowcover at Tianshan Number 1 Glacier and its Relation to Climate and Environment

The bacterial distribution, and its relationship with climate and environment factors were investigated in the snowcover at Tianshan Number 1 Glacier. The results showed that psychrotrophs were the preponderant bacteria in pit samples, though they were not the dominant species in the new fallen snow. The quantity and diversity of the cultivable bacteria decreased with the passage of time, indicating that the bacterial community acclimatized to low temperature by changing its structure. During this time, the peak number of the cultivable bacteria was associated with dirt layers, indicating that the bacterial input came with dust. Concurrently, the quantity and diversity of the cultivable bacteria showed a trend of variation similar to that shown by the δ18O values and the soluble ion concentrations, indicating that the bacterial distribution was related to both temperature and the amount of dust transported onto the glacier. Phylogentic analyses of 16S rRNA indicated that all the isolates fell into six categories: α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, Cytophaga-Flavobacterium-Bacteroides (CFB) group bacteria, high G+C gram-positive bacteria, and low G+C gram-positive bacteria. In the snow pit, the abundance of the CFB group bacteria (mainly of the genus Flavobacterium) decreased from 55.5% to 1.49% with age, and fluctuated similar to the ion concentrations and the δ18O value. Meanwhile the α-Proteobacteria (mainly of the genus Brevundimonas) increased from 0.9% to 88.1%, indicating that Brevundimonas was the dominant psychrotroph in the study area, whose abundance varied inversely compared to the above-mentioned chemical properties. All the results suggest that bacterial abundance and diversity vary with climate and the physical chemical microenvironment. The pattern of bacterial distribution could be a biological index for the record of climate and environment change in the Tianshan Number 1 Glacier.

Diversity of Prokaryotic Communities Indigenous to Acid Mine Drainage and Related Rocks from Baiyin Open-Pit Copper Mine Stope, China

ABSTRACT Metagenomic approach permits us to obtain the latent resources from culturable and unculturable microorganisms in ecosystem. In this study, high-throughput sequencing was practiced to comprehensively probe prokaryotic community within extreme acidic environment of Baiyin open-pit mine stope, which varied in pH and other physicochemical parameters. Bioinformatics analysis was further accomplished to process millions of Illumina reads and analyzed alpha and beta diversities, and prokaryotic community profile in different samples obtained from the acidic mine stope. Diversity indices such as ACE, Chao, Shannon, and Simpson were varied among samples. Both taxon richness and evenness were significantly higher in the solid samples than that of the water samples. Taxonomic diversity was unexpectedly higher within confined pit ecosystem. Most of the sequences were assigned to phyla Proteobacteria, Firmicutes, and Acidobacteria. In archaea, Euryarchaeota and Thaumarchaeota were major phyla reported, however, archaea occupied very little share in the metagenome. At class level, variation in community structure was higher within samples. Among iron- and sulfur-related acidophiles, 30.8% of the sequences were unidentified at genera level, while the remaining were dominated by sulfur and/or iron oxidizing Acidithiobacillus and heterotrophic Acidiphilum related groups. The community profile of solid and water groups was different and metagenomic biomarkers were higher in solid, while acidophiles and archaea were reported only in water group by using LEfSe. Among samples, community structure and abundance was varied in terms of OTUs abundance, which clearly indicates spatial variation and proposed the influence of physicochemical and geochemical properties on phylogenetic diversity. This study offers numerous treasured datasets for better understanding the community composition under the influence of geochemical and physicochemical factors and possible novelty in terms of taxonomic/phylogenetic diversity in acidic ecosystem.

Complete genome sequence of Acinetobacter sp. TTH0-4, a cold-active crude oil degrading strain isolated from Qinghai-Tibet Plateau

Acinetobacter sp. strain TTH0-4 was isolated from a permafrost region in Qinghai-Tibet Plateau. With its capability to degrade crude oil at low temperature, 10°C, the strain could be an excellent candidate for the bioremediation of crude oil pollution in cold areas or at cold seasons. We sequenced and annotated the whole genome to serve as a basis for further elucidation of the genetic background of this promising strain, and provide opportunities for investigating the metabolic and regulatory mechanisms and optimizing the biodegradative activity in cold environment.