Phylogenetic diversity of bacteria isolates from the Qinghai-Tibet Plateau permafrost region

The Qinghai-Tibet Plateau in east Asia is a unique and important permafrost environment. However, its microbiology remains largely unexplored to date. In this study, sediment samples were collected from the Qinghai-Tibet Plateau permafrost region, bacteria isolation procedures were performed 8 times, and the samples incubated at 4 degrees C for nearly 3 months. The number of colony forming units (cfu) ranged from 0 to 10(7)/(g dry soil). The quantity of culturable bacteria grew exponentially within the first few weeks, and then slowed gradually to a plateau. Phylogenetic analyses indicated that all the isolates fell into 6 categories: high G+C Gram-positive bacteria, low G+C Gram-positive bacteria, alpha-Proteobacteria, beta-Proteobacteria, gamma-Proteobacteria, and Cytophaga-Flavobacterium-Bacteroides group bacteria. The isolates belong to 19 genera, but the genera Arthrobacter and Pseudomonas were predominant. With the increase in incubation time, the isolated populations changed in terms of both species and their respective quantities. Of the 33 analyzed isolates, 9 isolates related to 8 genera might be new taxa. These results suggest that the Qinghai-Tibet Plateau permafrost region is a specific ecologic niche that accommodates an original microbial assemblage.     

Response of Soil Bacterial Community Structure to Permafrost Degradation in the Upstream Regions of the Shule River Basin,Qinghai–Tibet Plateau

Permafrost degradation affects soil properties and vegetation, but little is known about its consequent effects on the soil bacterial community. In this study, we analyzed the bacterial community structure of 12 permafrost-affected soil samples from four principal permafrost types, sub-stable permafrost (SSP), transition permafrost (TP), unstable permafrost (UP) and extremely unstable permafrost (EUP), to investigate the effects of vegetation characteristics and soil properties on bacterial community structure during the process of permafrost degradation. Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes were the predominant phyla in all four permafrost soil types. The relative abundance of Proteobacteria decreased in the order SSP > TP> UP > EUP, whereas the abundance of Actinobacteria increased in the order SSP < TP < UP < EUP. Moreover, the Actinobacteria/Proteobacteria ratio increased significantly in the order SSP < TP < UP < EUP along with permafrost degradation, which may be useful as a sign of permafrost degradation. Redundancy analysis (RDA) showed that bacterial communities could be clustered by permafrost types. Analysis of single factors revealed that soil moisture (SM) was the most important factor affecting the bacterial community structure and diversity, followed by soil total nitrogen (STN) and vegetation cover (VC). Partial RDA analysis showed that the soil properties and vegetation characteristics jointly shaped the bacterial community structure. Hence, we can conclude that permafrost degradation, caused by global warming, affects vegetation and soil properties and consequently drives changes in the soil bacterial community structure.     

Bioleaching of copper- and zinc-bearing ore using consortia of indigenous iron-oxidizing bacteria

Indigenous iron-oxidizing bacteria were isolated on modified selective 9KFe²⁺ medium from Baiyin copper mine stope, China. Three distinct acidophilic bacteria were isolated and identified by analyzing the sequences of 16S rRNA gene. Based on published sequences of 16S rRNA gene in the GenBank, a phylogenetic tree was constructed. The sequence of isolate WG101 showed 99% homology with Acidithiobacillus ferrooxidans strain AS2. Isolate WG102 exhibited 98% similarity with Leptospirillum ferriphilum strain YSK. Similarly, isolate WG103 showed 98% similarity with Leptospirillum ferrooxidans strain L15. Furthermore, the biotechnological potential of these isolates in consortia form was evaluated to recover copper and zinc from their ore. Under optimized conditions, 77.68 ± 3.55% of copper and 70.58 ± 3.77% of zinc were dissolved. During the bioleaching process, analytical study of pH and oxidation–reduction potential fluctuations were monitored that reflected efficient activity of the bacterial consortia. The FTIR analysis confirmed the variation in bands after treatment with consortia. The impact of consortia on iron speciation within bioleached ore was analyzed using Mössbauer spectroscopy and clear changes in iron speciation was reported. The use of indigenous bacterial consortia is more efficient compared to pure inoculum. This study provided the basic essential conditions for further upscaling bioleaching application for metal extraction.

     

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

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.     

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.     

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 and distribution of alkaliphilic psychrotolerant bacteria in the Qinghai–Tibet Plateau permafrost region

The Qinghai–Tibet Plateau represents a unique permafrost environment, being a result of high elevation caused by land uplift. And the urgency was that plateau permafrost was degrading rapidly under the current predicted climatic warming scenarios. Hence, the permafrost there was sampled to recover alkaliphilic bacteria populations. The viable bacteria on modified PYGV agar were varied between 10² and 10⁵ CFU/g of dry soil. Forty-eight strains were gained from 18 samples. Through amplified ribosomal DNA restriction analysis (ARDRA) and phylogenetic analyses, these isolates fell into three categories: high G + C gram positive bacteria (82.3%), low G + C gram positive bacteria (7.2%), and gram negative α-proteobacteria (10.5%). The strains could grow at pH values ranging from 6.5 to 10.5 with optimum pH in the range of 9–9.5. Their growth temperatures were below 37°C and the optima ranging from 10 to 15°C. All strains grew well when NaCl concentration was below 15%. These results indicate that there are populations of nonhalophilic alkaliphilic psychrotolerant bacteria within the permafrost of the Qinhai-Tibet plateau. The abilities of many of the strains to produce extracellular protease, amylase and cellulase suggest that they might be of potential value for biotechnological exploitation.     

Microbial community structure along an altitude gradient in three different localities

The microbial community structure along an altitude gradient was investigated in different localities, in Kalasi lake, Urumqi river and Sangong river, Xingjiang (China). The mean numbers of DAPI (4',6-diamidino-2-phenylindole)-stained cells were lower in Kalasi lake than that in Urumqi river and Sangong river; these differences were attributed to increasing environmental harshness including lower soil organic carbon and nitrogen content, more acidic pH and lower annual temperature. In each locality, the numbers of bacteria and archaea measured with two fluorescence-labeled 16S rRNA oligonucleotide probes (EUB338 and ARCH915) were higher in a coniferous forest and lower in desert vegetation. A significant and positive relationship was found between microbial and soil organic carbon and total nitrogen along the altitudinal gradient, indicating that plant communities and soil nutrients influence the soil microbial structure. The results show that the microbial population in higher latitudinal site was fewer than lower latitudinal one, soil microorganisms were positively correlated to soil organic carbon and total nitrogen, and plant communities had an obviously impact on soil microbes.     

Characterization of the genome of a Nocardia strain isolated from soils in the Qinghai-Tibetan Plateau that specifically degrades crude oil and of this biodegradation

A strain of Nocardia isolated from crude oil-contaminated soils in the Qinghai-Tibetan Plateau degrades nearly all components of crude oil. This strain was identified as Nocardia soli Y48, and its growth conditions were determined. Complete genome sequencing showed that N. soli Y48 has a 7.3 Mb genome and many genes responsible for hydrocarbon degradation, biosurfactant synthesis, emulsification and other hydrocarbon degradation-related metabolisms. Analysis of the clusters of orthologous groups (COGs) and genomic islands (GIs) revealed that Y48 has undergone significant gene transfer events to adapt to changing environmental conditions (crude oil contamination). The structural features of the genome might provide a competitive edge for the survival of N. soli Y48 in oil-polluted environments and reflect the adaptation of coexisting bacteria to distinct nutritional niches.     

珠穆朗玛峰北坡可培养石生细菌多样性及抗紫外辐射能力

【背景】珠穆朗玛峰地区具有寒冷低温、强辐射等极端环境条件,珠穆朗玛峰北坡石生微生物研究未见报道。【目的】针对珠穆朗玛峰北坡石生微生物开展研究,阐明珠穆朗玛峰北坡石生生境中可培养细菌多样性,开发珠穆朗玛峰北坡抗紫外辐射菌株资源。【方法】通过可培养法、16S rRNA基因序列分析方法以及紫外辐射筛选对珠穆朗玛峰北坡可培养石生细菌多样性以及抗紫外辐射能力进行研究。【结果】从珠穆朗玛峰北坡石生生境中共分离获得52株石生细菌,归类为放线菌门(Actinobacteria)、厚壁菌门(Firmicutes)、变形菌门(Proteobacteria)和拟杆菌门(Bacteroidetes),其中放线菌门和变形菌门为优势菌门,鞘脂单胞菌属、节杆菌属、链霉菌属为优势菌属,有2株菌为潜在新种。从已分离鉴定菌株中筛选出了2株抗紫外辐射能力较高的菌株,分别是芽孢杆菌属菌株ZFBP4009和链霉菌属菌株ZFBP1009。【结论】珠穆朗玛峰北坡石生环境蕴含多样性丰富的石生细菌,所分离菌株抗紫外辐射能力突出,为揭示相关极端环境下微生物的分布特征及极端环境微生物资源开发提供了数据支持及菌株资源。