Temporal variation of bacterial community and nutrients in Tibetan glacier snowpack

The Tibetan Plateau harbors the largest number of glaciers outside the polar regions, which are the source of several major rivers in Asia. These glaciers are also major sources of nutrients for downstream ecosystems, while there is a little amount of data available on the nutrient transformation processes on the glacier surface. Here, we monitored the carbon and nitrogen concentration changes in a snowpit following a snowfall in the Dunde Glacier of the Tibetan Plateau. The association of carbon and nitrogen changes with bacterial community dynamics was investigated in the surface and subsurface snow (depth at 0–15 and 15–30 cm, respectively) during a 9 d period. Our results revealed rapid temporal changes in nitrogen (including nitrate and ammonium) and bacterial communities in both surface and subsurface snow. Nitrate and ammonium concentrations increased from 0.44 to 1.15 mg L−1 and 0.18 to 0.24 mg L−1 in the surface snow and decreased from 3.81 to 1.04 and 0.53 to 0.25 mg L−1 in the subsurface snow over time. Therefore, we suggest that the surface snow is not nitrogen-limited, while the subsurface snow is associated with nitrogen consumption processes and is nitrogen-limited. The nitrate concentration co-varied with bacterial diversity, community structure, and the predicted nitrogen fixation and nitrogen assimilation/denitrification-related genes (narG), suggesting nitrogen could mediate bacterial community changes. The nitrogen limitation and enriched denitrification-related genes in subsurface snow suggested stronger environmental and biotic filtering than those in surface snow, which may explain the lower bacterial diversity, more pronounced community temporal changes, and stronger biotic interactions. Collectively, these findings advance our understanding of bacterial community variations and bacterial interactions after snow deposition and provide a possible biological explanation for nitrogen dynamics in snow

Temporal variation of bacterial community and nutrients in Tibetan glacier snowpack

The Tibetan Plateau harbors the largest number of glaciers outside the polar regions, which are the source of several major rivers in Asia. These glaciers are also major sources of nutrients for downstream ecosystems, while there is a little amount of data available on the nutrient transformation processes on the glacier surface. Here, we monitored the carbon and nitrogen concentration changes in a snowpit following a snowfall in the Dunde Glacier of the Tibetan Plateau. The association of carbon and nitrogen changes with bacterial community dynamics was investigated in the surface and subsurface snow (depth at 0-15 and 15-30 cm, respectively) during a 9 d period. Our results revealed rapid temporal changes in nitrogen (including nitrate and ammonium) and bacterial communities in both surface and subsurface snow. Nitrate and ammonium concentrations increased from 0.44 to 1.15 mg L-1 and 0.18 to 0.24 mg L-1 in the surface snow and decreased from 3.81 to 1.04 and 0.53 to 0.25 mg L-1 in the subsurface snow over time. Therefore, we suggest that the surface snow is not nitrogen-limited, while the subsurface snow is associated with nitrogen consumption processes and is nitrogen-limited. The nitrate concentration co-varied with bacterial diversity, community structure, and the predicted nitrogen fixation and nitrogen assimilation/denitrification-related genes (narG), suggesting nitrogen could mediate bacterial community changes. The nitrogen limitation and enriched denitrification-related genes in subsurface snow suggested stronger environmental and biotic filtering than those in surface snow, which may explain the lower bacterial diversity, more pronounced community temporal changes, and stronger biotic interactions. Collectively, these findings advance our understanding of bacterial community variations and bacterial interactions after snow deposition and provide a possible biological explanation for nitrogen dynamics in snow

Bacteria in the lakes of the Tibetan Plateau and polar regions

The Tibetan Plateau, also termed ‘the Third Pole’ harbors the largest number of high-altitude lakes in the world. Due to the presence of extreme conditions such as low temperature and oligotrophy, the lakes of the Tibetan Plateau share environmental features in common with lakes in the polar regions. However, the extent to which these environments are analogous, or indeed whether they harbor similar microbial communities or a high level of endemic species is poorly understood. Here we compared high-throughput 16S rRNA gene sequencing data from the lakes of the three different regions in order to characterize their taxonomic diversity, the community composition and biogeography. Our results showed despite the similarity in environmental conditions, the spatial distribution of the bacterial communities was distinct with only 3.1% of all operational taxonomic units (OTUs) being present in all three regions (although these OTUs did account for a considerable proportion of the total sequences, 36.4%). Sequences belonging to Burkholderiales and Actinomycetales dominated the shared OTUs across all three regions. Scale dependent distance decay patterns provided evidence of dispersal limitation. Climatic variables and dispersal limitation were apparently both important in controlling the spatial distribution of bacterial communities across regions. This work expands our understanding of the diversity and biogeography of lake bacterial communities across the Tibetan Plateau and provides insights into how they compare to those of the Antarctic and Arctic

Anthropogenic impact on airborne bacteria of the Tibetan Plateau

The Tibetan Plateau is a pristine environment with limited human disturbance, with its aerosol microbiome being primarily influenced by the monsoon and westerly circulations. Additionally, the diversity and abundance of airborne microorganisms are also affected by anthropogenic activities, such as animal farming, agriculture, and tourism, which can lead to increased risks to the ecosystem and human health. However, the impact of anthropogenic activities on airborne microbes on the Tibetan Plateau has been rarely studied. In this work, we investigated the airborne bacteria of areas with weak (rural glacier) and strong human disturbance (urban building), and found that anthropogenic activities increased the diversity of airborne bacteria, and the concentration of potential airborne pathogens. Moreover, airborne bacteria in rural aerosols demonstrated significant differences in their community structure during monsoon- and westerly-affected seasons, while this pattern was weakened in urban aerosols. Additionally, urban aerosols enriched Lactobacillus sp. (member of genus Lactobacillus), which are potential pathogens from anthropogenic sources, whereas rural aerosols enriched A. calcoaceticus (member of genus Acinetobacter) and E. thailandicus (member of genus Enterococcus), which are both speculated to be sourced from surrounding animal farming. This study evaluated the impact of human activities on airborne bacteria in the Tibetan Plateau and contributed to understanding the enrichment of airborne pathogens in natural and anthropogenic background

Genomic, proteomic and bioinformatic analysis of two temperate phages in Roseobacter clade bacteria isolated from the deep-sea water

Abstract Background Marine phages are spectacularly diverse in nature. Dozens of roseophages infecting members of Roseobacter clade bacteria were isolated and characterized, exhibiting a very high degree of genetic diversity. In the present study, the induction of two temperate bacteriophages, namely, vB_ThpS-P1 and vB_PeaS-P1, was performed in Roseobacter clade bacteria isolated from the deep-sea water, Thiobacimonas profunda JLT2016 and Pelagibaca abyssi JLT2014, respectively. Two novel phages in morphological, genomic and proteomic features were presented, and their phylogeny and evolutionary relationships were explored by bioinformatic analysis. Results Electron microscopy showed that the morphology of the two phages were similar to that of siphoviruses. Genome sequencing indicated that the two phages were similar in size, organization, and content, thereby suggesting that these shared a common ancestor. Despite the presence of Mu-like phage head genes, the phages are more closely related to Rhodobacter phage RC1 than Mu phages in terms of gene content and sequence similarity. Based on comparative genomic and phylogenetic analysis, we propose a Mu-like head phage group to allow for the inclusion of Mu-like phages and two newly phages. The sequences of the Mu-like head phage group were widespread, occurring in each investigated metagenomes. Furthermore, the horizontal exchange of genetic material within the Mu-like head phage group might have involved a gene that was associated with phage phenotypic characteristics. Conclusions This study is the first report on the complete genome sequences of temperate phages that infect deep-sea roseobacters, belonging to the Mu-like head phage group. The Mu-like head phage group might represent a small but ubiquitous fraction of marine viral diversity

Bacterial community changes in a glacial-fed Tibetan lake are correlated with glacial melting

Climate change-induced glacial melting is a global phenomenon. The effects of climate change-induced melting on the microbial ecology in different glacial-fed aquatic systems have been well illuminated, but the resolution of seasonal dynamics was still limited. Here, we studied bacterial community composition and diversity in a glacial-fed Tibetan lake, Lake Ranwu, to elucidate how glacial-fed aquatic ecosystems respond to the seasonal glacial melting. Obvious seasonal variations of bacterial dominant groups were found in Lake Ranwu and inlet rivers. In April, the majority of OTUs belonged to the Bacteroidetes, Actinobacteria and Proteobacteria. The Proteobacteria increased to the most abundant phylum in July and November, while the Bacteroidetes and Actinobacteria decreased about 50% over seasons. Most key discriminant taxa of each season's community strongly associated with specific environmental variables, suggesting their adaptation to seasonal environments. Bacterial alpha diversity varied among seasons and exhibited strongly negative correlations with conductivity. Conductivity was the major driving force in determining the seasonal variation of bacterial community composition. Fluctuated conductivity was one of the consequences of seasonal melting of glaciers. This study offered evidence for the unique seasonal dynamics pattern of bacterial communities responding to glacial melting. Moreover, this study may provide a reference for assessing the long-term effects of glacial retreat on glacial-fed aquatic ecosystems. (C) 2018 Elsevier B.V. All rights reserved

Gramella flava sp nov, a member of the family Flavobacteriaceae isolated from seawater

National Key Basic Research Program of China [2011CB808800]; 863 Program [2012AA092003]; National Natural Science Foundation of China [41191021, 41276131]A novel Gram-negative, yellow-pigmented, aerobic, motile by gliding, rod-shaped marine bacterium (JLT2011(T)) was isolated from surface seawater. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JLT2011(T) could be assigned to the genus Gramella and was most closely related to Gramella gaetbulicola, with 96.2% similarity. The genomic DNA G+C content was 42.1%. The predominant fatty acids were C-16:0, iso-C-15:0, C-18:0 and summed feature 3 (C-16:1 omega 6c/C-16:1 omega 7c). The major menaquinone was MK-6. The major components of the polar lipid profile were phosphatidylglycerol, diphosphatidylglycerol and sphingoglycolipid. On the basis of phenotypic, genotypic and taxonomic data presented, strain JLT2011(T) is considered to represent a novel species of the genus Gramella, for which the name Gramella flava sp. nov. is proposed; the type strain is JLT2011(T) (=CGMCC 1.12375(T)=LMG 27360(T))

Distribution and Functions of TonB-Dependent Transporters in Marine Bacteria and Environments: Implications for Dissolved Organic Matter Utilization

Background: Bacteria play critical roles in marine nutrient cycles by incorporating and redistributing dissolved organic matter (DOM) and inorganic nutrients in the ocean. TonB-dependent transporter (TBDT) proteins allow Gram-negative bacteria to take up scarce resources from nutrient-limiting environments as well as siderophores, heme, vitamin B12, and recently identified carbohydrates. Thus, the characterization of TBDT distribution and functions is essential to better understand the contribution TBDT to DOM assimilation and its consequences on nutrient cycling in the environment. Methodology/Principal Findings: This study presents the distribution of encoded known and putative TBDT proteins in the genomes of microorganisms and from the Global Ocean Survey data. Using a Lek clustering algorithm and substrate specificities, the TBDT sequences were mainly classified into the following three groups: (1) DOM transporters; (2) Siderophores/Vitamins transporters; and (3) Heme/Hemophores/Iron(heme)-binding protein transporters. Diverse TBDTs were found in the genomes of oligotroph Citromicrobium bathyomarinum JL354 and Citromicrobium sp JLT1363 and were highly expressed in the stationary phase of bacterial growth. The results show that the Gammaproteobacteria and the Cytophaga-Flavobacterium-Bacteroides (CFB) group bacteria accounted for the majority of the TBDT gene pool in marine surface waters. Conclusions/Significance: The results of this study confirm the ecological importance of TBDTs in DOM assimilation for bacteria in marine environments owing to a wide range of substrate utilization potential in the ubiquitous Gammaproteobacteria and CFB group bacteria.NSFC (Natural Science Foundation of China) [40906079]; National Basic Research Program of China [2011CB808800]; NSFC [91028001]; Public Science and Technology Research Funds Projects of Ccean [201105021]; Scientific Research Foundation for Returned Scholars, Ministry of Education of Chin

Oceanitalea nanhaiensis gen nov, sp nov, an actinobacterium isolated from seawater

NSFC [91028001, 41076063]; SOA [201105021]A Gram-positive, motile, short-rod-shaped bacterium, designated strain JLT1488(T), was isolated from the South China Sea and investigated in a taxonomic study using a polyphasic approach. The peptidoglycan type determined for strain JLT1488(T) was A4 alpha with lysine as the diagnostic cell-wall diamino acid and an interpeptide bridge of L-Lys L-Glu. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, an unknown glycolipid and an unknown phospholipid. The only detected menaquinone was MK-8(H-4), and the major fatty acids were summed feature 8 (C-18:1 omega 7c/C-18:1 omega 6C) C-16:0 and summed feature 3 (C-16:1 omega 7c/C-16:1 omega 6c); significant amounts of C-12:0 3-OH, C-10:0 and C-19:0 cyclo omega 8c were also present. The G + C content of the genomic DNA was 62.3 mol%. Comparison of the 16S rRNA gene sequence of strain JLT1488(T) with those of related type strains demonstrated that it represented a novel lineage within the family Bogoriellaceae, suborder Micrococcineae, being closely related to species of the genera Georgenia, Bogoriella and Cellulomonas (94.6-96.8% sequence similarity). These results demonstrate that strain JLT1488T is a member of a new genus, for which the name Oceanitalea nanhaiensis gen. nov., sp. nov. is proposed. The type strain of the type species is JLT1488(T) (=JCM 17755(T)=CGMCC 1.10826(T))