Bacterial Activity in South Pole Snow

Large populations (200 to 5,000 cells ml⁻¹ in snowmelt) of bacteria were present in surface snow and firn from the south pole sampled in January 1999 and 2000. DNA isolated from this snow yielded ribosomal DNA sequences similar to those of several psychrophilic bacteria and a bacterium which aligns closely with members of the genus Deinococcus, an ionizing-radiation- and desiccation-resistant genus. We also obtained evidence of low rates of bacterial DNA and protein synthesis which indicates that the organisms were metabolizing at ambient subzero temperatures (−12 to −17°C).     

Possible quorum sensing in marine snow bacteria: production of acylated homoserine lactones by Roseobacter strains isolated from marine snow

We report here, for the first time, that bacteria associated with marine snow produce communication signals involved in quorum sensing in gram-negative bacteria. Four of 43 marine microorganisms isolated from marine snow were found to produce acylated homoserine lactones (AHLs) in well diffusion and thin-layer chromatographic assays based on the Agrobacterium tumefaciens reporter system. Three of the AHL-producing strains were identified by 16S ribosomal DNA gene sequence analysis as Roseobacter spp., and this is the first report of AHL production by these alpha-PROTEOBACTERIA: It is likely that AHLs in Roseobacter species and other marine snow bacteria govern phenotypic traits (biofilm formation, exoenzyme production, and antibiotic production) which are required mainly when the population reaches high densities, e.g., in the marine snow community.     

Microbial Community Structure, Pigment Composition, and Nitrogen Source of Red Snow in Antarctica

“Red snow” refers to red-colored snow, caused by bloom of cold-adapted phototrophs, so-called snow algae. The red snow found in Langhovde, Antarctica, was investigated from several viewpoints. Various sizes of rounded red cells were observed in the red snow samples under microscopy. Pigment analysis demonstrated accumulation of astaxanthin in the red snow. Community structure of microorganisms was analyzed by culture-independent methods. In the analyses of small subunit rRNA genes, several species of green algae, fungus, and various phylotypes of bacteria were detected. The detected bacteria were closely related to psychrophilic or psychrotolerant heterotrophic strains, or sequences detected from low-temperature environments. As predominant lineage of bacteria, members of the genus Hymenobacter were consistently detected from samples obtained in two different years. Nitrogen isotopic compositions analysis indicated that the red snow was significantly ¹⁵N-enriched. Based on an estimation of trophic level, it was suggested that primary nitrogen sources of the red snow were supplied from fecal pellet of seabirds including a marine top predator of Antarctica.     

Isolation and characterization of polymorphic microsatellite markers in the red snow crab (Chionoecetes japonicus)

A total of 12 polymorphic microsatellite DNA loci were isolated from the red snow crab, Chionoecetes japonicus (Brachyura: Majidae), one of important fisheries resources in the Far East. The number of alleles observed at each locus ranged from two to 19, with the observed and expected heterozygosities of 0.125-0.875 and 0.156-0.949, respectively, suggesting these loci to be a useful molecular marker for population analysis in this species. Of the 12 loci, seven also were available for genotyping of the snow crab, Chionoecetes opilio, implying these loci as a useful molecular marker in the genus Chionoecetes.     

Possible Quorum Sensing in Marine Snow Bacteria: Production of Acylated Homoserine Lactones by Roseobacter Strains Isolated from Marine Snow

We report here, for the first time, that bacteria associated with marine snow produce communication signals involved in quorum sensing in gram-negative bacteria. Four of 43 marine microorganisms isolated from marine snow were found to produce acylated homoserine lactones (AHLs) in well diffusion and thin-layer chromatographic assays based on the Agrobacterium tumefaciens reporter system. Three of the AHL-producing strains were identified by 16S ribosomal DNA gene sequence analysis as Roseobacter spp., and this is the first report of AHL production by these α-Proteobacteria. It is likely that AHLs in Roseobacter species and other marine snow bacteria govern phenotypic traits (biofilm formation, exoenzyme production, and antibiotic production) which are required mainly when the population reaches high densities, e.g., in the marine snow community.     

Molecular phylogenetic relationship of snow finch complex (genera Montifringilla, Pyrgilauda, and Onychostruthus) from the Tibetan plateau

The snow finch complex (Montifringilla, Pyrgilauda, and Onychostruthus) has its center of distribution on the Tibetan plateau, with six out of seven species in the genera occurring there. Phylogenetic relationships among these six species of three genera have been studied based on DNA sequence data obtained from the mitochondrial cytochrome b gene and the nuclear myoglobin gene. The results support monophyly of the snow finch complex group and three major evolutionary lineages are recognized. The first clade consists of ruficollis, blanfordi, and davidiana. These three taxa are sometimes placed in their own genus, Pyrgilauda, and the DNA data supports this. The three taxa nivalis, henrici, and adamsi have traditionally been placed in the genus Montifringilla, and they group together strongly in the present analysis. The results further suggest that nivalis and adamsi are more closely related to each other than are nivalis and henrici, despite that the latter two are often regarded as conspecific. The third distinct lineage within the snow finch complex consists of taczanowskii, which has been placed its own genus, Onychostruthus. This taxon has a basal position in the phylogenetic tree and is sister to all other snow finches. We estimated that taczanowskii split from the other taxa between 2 and 2.5 mya, i.e., about the time for the most recent uplift of the Tibetan plateau, "the Tibet movement", 3.6-1.7 mya. Cladogenesis within the Montifringilla and Pyrgilauda clades seems to be contemporary with the second phase of "Tibet movement" at 2.5 mya and the third phase at 1.7 mya and "Kunhuang movement" in 1.5-0.6 mya. The dramatic climatic and ecological changes following from the uplift of the Tibetan plateau, together with the cyclic contraction and expansion of suitable habitats during the Pleistocene, are probably the most important factors for the cladogenesis in snow finch complex.     

Diversity and characterization of mercury-resistant bacteria in snow, freshwater and sea-ice brine from the High Arctic

It is well-established that atmospheric deposition transports mercury from lower latitudes to the Arctic. The role of bacteria in the dynamics of the deposited mercury, however, is unknown. We characterized mercury-resistant bacteria from High Arctic snow, freshwater and sea-ice brine. Bacterial densities were 9.4 × 10(5), 5 × 10(5) and 0.9-3.1 × 10(3) cells mL(-1) in freshwater, brine and snow, respectively. Highest cultivability was observed in snow (11.9%), followed by freshwater (0.3%) and brine (0.03%). In snow, the mercury-resistant bacteria accounted for up to 31% of the culturable bacteria, but <2% in freshwater and brine. The resistant bacteria belonged to the Alpha-, Beta- and Gammaproteobacteria, Firmicutes, Actinobacteria, and Bacteriodetes. Resistance levels of most isolates were not temperature dependent. Of the resistant isolates, 25% reduced Hg(II) to Hg(0). No relation between resistance level, ability to reduce Hg(II) and phylogenetic group was observed. An estimation of the potential bacterial reduction of Hg(II) in snow suggested that it was important in the deeper snow layers where light attenuation inhibited photoreduction. Thus, by reducing Hg(II) to Hg(0), mercury-resistant bacteria may limit the supply of substrate for methylation processes and, hence, contribute to lowering the risk that methylmercury is being incorporated into the Arctic food chains.     

崇测冰帽不同的冰川样品可培养细菌群落结构差异北大核心CSCD

【目的】研究细菌群落组成在西昆仑崇测冰帽冰川雪样、冰碛物和土样中的差异。【方法】通过传统的纯培养和菌株16S r RNA基因序列鉴定,分析菌株在门水平和属水平的群落结构。【结果】冰川细菌由Actinobacteria、Firmicutes、Proteobacteria和Bacteroidetes 4个门组成。雪样以Proteobacteria为优势,而土样和冰碛物则以Actinobacteria为优势。在属的水平上,冰川土样中的优势属仅有Arthrobacter,雪样中的优势属主要有Methylobacterium、Modestobacter、Hymenobacter、Brevundimonas、Bacillus这5种。雪环境的细菌群落结构与冰碛物和土样的差异性较大,而冰碛物和土样之间的差异性不大。Skermanella可能为崇测冰帽所特有的细菌。【结论】初步说明了在冰川退缩的气候环境下,冰川雪样细菌多样性的脆弱性,以及冰川雪环境细菌资源保护的重要性。     

Bacterial characterization of the snow cover at Spitzberg, Svalbard

A sampling campaign was organized during spring 2004 in Spitzberg, Svalbard, in the area around the scientific base of Ny-Alesund, to characterize the snow pack bacterial population. Total bacteria counts were established by 4',6-diamino-2-phenylindole (DAPI) in the seasonal snow pack bordering the sea. On the sea shore, bacterial concentration was about 6 x 10(4) cells mL(-1), without any significant variation according to depth. In the accumulation snow layer of the glacier, concentrations were about 2 x 10(4 )cells mL(-1), except in the 2003 summer layer, where it reached 2 x 10(5) cells mL(-1), as the result of cell multiplication allowed by higher temperature and snow melting. Strains isolated from the seasonal snow pack were identified from their 16S rRNA gene sequences, and lodged in GenBank. They belong to the Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria, Firmicutes and Actinobacteria. They are closely related to cold environment bacteria, as revealed by phylogenetic tree constructions, and two appear to be of unknown affiliation. Using 1H nuclear magnetic resonance, it was shown that these isolates have the capacity to degrade organic compounds found in Arctic snow (propionate, acetate and formate), and this can allow them to develop when snow melts, and thus to be actively involved in snow chemistry.     

The dynamic bacterial communities of a melting High Arctic glacier snowpack

Snow environments can occupy over a third of land surface area, but little is known about the dynamics of snowpack bacteria. The effect of snow melt on bacterial community structure and diversity of surface environments of a Svalbard glacier was examined using analyses of 16S rRNA genes via T-RFLP, qPCR and 454 pyrosequencing. Distinct community structures were found in different habitat types, with changes over 1 week apparent, in particular for the dominant bacterial class present, Betaproteobacteria. The differences observed were consistent with influences from depositional mode (snowfall vs aeolian dusts), contrasting snow with dust-rich snow layers and near-surface ice. Contrary to that, slush as the decompositional product of snow harboured distinct lineages of bacteria, further implying post-depositional changes in community structure. Taxa affiliated to the betaproteobacterial genus Polaromonas were particularly dynamic, and evidence for the presence of betaproteobacterial ammonia-oxidizing bacteria was uncovered, inviting the prospect that the dynamic bacterial communities associated with snowpacks may be active in supraglacial nitrogen cycling and capable of rapid responses to changes induced by snowmelt. Furthermore the potential of supraglacial snowpack ecosystems to respond to transient yet spatially extensive melting episodes such as that observed across most of Greenland''s ice sheet in 2012 merits further investigation.     

Seasonal change in bacterial flora and biomass in mountain snow from the Tateyama Mountains, Japan, analyzed by 16S rRNA gene sequencing and real-time PCR

The bacterial flora and biomass in mountain snow from the Tateyama Mountains, Toyama Prefecture, Japan, one of the heaviest snowfall regions in the world, were analyzed by amplified ribosomal DNA restriction analysis followed by 16S rRNA gene sequencing and DNA quantification by real-time PCR. Samples of surface snow collected in various months during the melting season contained a psychrophilic bacterium, Cryobacterium psychrophilum, and two psychrotrophic bacteria, Variovorax paradoxus and Janthinobacterium lividum. Bacterial colonies that developed in an in situ meltwater medium at 4 degrees C were revealed to be V. paradoxus. The biomasses of C. psychrophilum, J. lividum, and V. paradoxus, as estimated by real-time PCR, showed large increases during the melting season from March to October (2.0 x 10(5)-fold, 1.5 x 10(5)-fold, and 1.0 x 10(4)-fold increases, respectively), suggesting their rapid growth in the surface snow. The biomasses of C. psychrophilum and J. lividum increased significantly from March to April, reached a maximum in August, and dropped at the end of the melting season. In contrast, the biomass of V. paradoxus did not increase as rapidly during the early melting season but continued to increase from June until October. The differences in development observed among these bacterial species suggest that their growth was promoted by different nutrients and/or environmental conditions in the snow. Since these three types of bacteria have also been reported to be present in a glacier in Antarctica and a Greenland ice core, they seem to be specialized members of the snow biota that are distributed in snow and ice environments in various parts of the world.     

Phylogenetic analysis of rumen bacteria by comparative sequence analysis of cloned 16S rRNA genes

Comparative DNA sequence analysis of 16S rRNA genes (rDNA) was undertaken to further our understanding of the make-up of bacterial communities in the rumen fluid of dairy cattle. Total DNA was extracted from the rumen fluid of 10 cattle fed haylage/corn silage/concentrate rations at two different times. Rumen samples were collected on two separate occasions from five cows each. In experiment 1, 31 cloned rDNA sequences were analysed. In experiment 2, DNA extractions were amplified using either 12 or 30 cycles of PCR in order to examine biases introduced during the reactions. A set of 53 sequences were analysed in experiment 2 from DNA amplified using 12 cycles and 49 sequences from PCR using 30 cycles. Sequences from the 5' end of 16S rRNA gene were compared with existing sequences in the Ribosomal Database Project. Clones from experiment 1 produced a data set in which 55% of the sequences were similar to low G+C Gram-positive bacteria related to the genus Clostridia, the majority of which were closely related to bacteria in Cluster XIV. Approximately 30% of the cloned sequences were related to bacteria in the Prevotella-Bacteroides group. Clones from experiment 2 produced a data set in which the majority of sequences were related to the Prevotella-Bacteroides group, regardless of the number of cycles of PCR. The remaining sequences clustered with members of the genus Clostridia. The majority of rDNA sequences analysed in this study represent novel rumen bacteria which have not yet been isolated.     

东天山地区庙儿沟雪坑中微生物多样性、群落结构与环境关系研究

通过荧光计数、恢复培养和变形梯度凝胶电泳(DGGE),分析了东天山地区庙儿沟不同深度积雪中的可培养细菌数量、多样性及其群落结构。结果表明,东天山地区冰雪微生物数量和多样性指数与气候环境替代指标钙离子、镁离子、氯离子等具有相关性。该地区雪坑中细菌隶属于4个不同系统发育群:proteobacteria(α-,β-,γ-),CFB,HGC和LGC,其中CFB类和proteobacteria类为主要类群。与青藏高原、南北极冰雪中微生物的比较分析发现Paracoccu和Aquasalina属是该地区的特殊微生物类群。直接培养和DGGE分析发现不同深度雪坑中微生物数量和群落结构都有明显的变化。结果表明,由于东天山地区的特殊地理位置,该地区冰雪微生物具有其特殊性。     

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.     

Community structure of microorganisms associated with reddish-brown iron-rich snow

Reddish-brown colored snow, containing spherical brown particles, has been observed in several mires in Japan. In order to characterize this remarkable phenomenon, the microbial community and chemical species in snow were analyzed. A core sample of snow which had a colored region was investigated and it revealed vertical shifts in physicochemical characteristics and the microbial community structure. The abundance of particles peaked within the colored layer, and correlated with the amount of reducible Fe(III). The interstitial water of the colored layer was enriched with Fe(II), and characterized by reduced concentration of dissolved methane. The bacterial community in the colored region was characterized by higher relative abundance of iron-reducing bacteria and methanotrophs. Aggregates of the brown particles were found as precipitates in snow melt pools, and were subjected to cloning analyses targeting several different genes. The majority of bacterial 16S rRNA gene clones belonged to the class Betaproteobacteria or the phylum Bacteroidetes. No snow algae were detected in the eukaryotic small subunit rRNA gene clone library. As a possible carbon source to sustain the community in the snow, involvements of carbon dioxide and methane were investigated by analyzing the genes involved in their assimilation. In the analyses of genes for ribulose-1,5-biphosphate carboxylase/oxygenase, clones related to sulfur oxidizers were obtained. The analysis of particulate methane monooxygenase genes indicated dominance of Methylobacter species. These results emphasized the uniqueness of this phenomenon, and iron reducers of the genus Geobacter are suggested to be the key organisms that could be investigated in order to understand the mechanism of this phenomenon.     

雪被去除对川西高山冷杉林冬季土壤微生物生物量碳氮和可培养微生物数量的影响

为了解气候变暖情景下雪被减少对冬季土壤微生物特征的影响,采用人工遮雪的方法,研究了雪被去除对原始冷杉林土壤微生物生物量和可培养微生物数量的影响.结果表明:雪被去除显著影响土壤微生物生物量碳(MBC)和氮(MBN)以及可培养细菌和真菌数量,但土壤微生物在雪被覆盖不同阶段具有不同的响应特征.在雪被去除处理下,土壤有机层MBC和MBN在雪被形成初期和雪被融化前期显著降低,而在雪被覆盖期和雪被融化后期显著增加;在雪被形成初期至雪被覆盖期,可培养细菌数量都显著降低,但可培养真菌数量都显著增加.雪被融化后,雪被去除显著降低土壤有机层MBC和可培养真菌数量,显著增加可培养细菌数量,对MBN无显著影响.矿质土壤层MBC、MBN和可培养微生物数量在雪被去除下的变化趋势与土壤有机层基本一致,但波动较小.雪被去除还改变了川西高山冷杉林冬季土壤微生物类群比,提高了土壤可培养真菌数量的冬季优势.     

Generic interrelations of purple bacteria in the genus Rhodopseudomonas

The technique of DNA--DNA hybridization was used to study relations offween purple nonsulfur bacteria (the family Rhodospirillaceae). The level of homologies with Rhodopseudomonas sphaeroides 8259 was nearly the same for different species (8-17%) in the genus Rhodopseudomonas under the conditions optimal for hybridization. The same level of homologies was found for the DNA of Rhodospirillum rubrum, a species belonging to another genus of purple nonsulfur bacteria (13%). Rhodomicrobium vannielli was most remote from R. sphaeroides 8259 (3%). Similar results were obtained under other conditions of hybridization. The intraspecial heterogeneity of R. sphaeroides was studied in this work. The thermal stability of hybrid duplexes was analysed. The results are indicative of a considerable divergence of different R. sphaeroides strains (delta T50 = 2.1-11.6).     

Comparison of cell-specific activity between free-living and attached bacteria using isolates and natural assemblages

Marine snow aggregates are microbial hotspots that support high bacterial abundance and activities. We conducted laboratory experiments to compare cell-specific bacterial protein production (BPP) and protease activity between free-living and attached bacteria. Natural bacterial assemblages attached to model aggregates (agar spheres) had threefold higher BPP and two orders of magnitude higher protease activity than their free-living counterpart. These observations could be explained by preferential colonization of the agar spheres by bacteria with inherently higher metabolic activity and/or individual bacteria increasing their metabolism upon attachment to surfaces. In subsequent experiments, we used four strains of marine snow bacteria isolates to test the hypothesis that bacteria could up- and down-regulate their metabolism while on and off an aggregate. The protease activity of attached bacteria was 10-20 times higher than that of free-living bacteria, indicating that the individual strains could increase their protease activity within a short time (2 h) upon attachment to surfaces. Agar spheres with embedded diatom cells were colonized faster than plain agar spheres and the attached bacteria were clustered around the agar-embedded diatom cells, indicating a chemosensing response. Increased protease activity and BPP allow attached bacteria to quickly exploit aggregate resources upon attachment, which may accelerate remineralization of marine snow and reduce the downward carbon fluxes.     

不同积雪覆盖期荒漠齿肋赤藓结皮层丛枝菌根真菌多样性变化

【背景】温带荒漠有积雪背景条件下的荒漠苔藓植物与丛枝菌根真菌(arbuscular mycorrhizal fungi,AMF)共生关系的研究非常有限。【目的】揭示不同积雪覆盖期(降雪前、雪盖期、融雪期)齿肋赤藓结皮层中AMF多样性的差异,为正确认识荒漠特色植物与微生物在冬季积雪期互利的重要生存策略提供数据支撑。【方法】利用高通量测序技术,分析稳定积雪期的古尔班通古特沙漠优势苔藓齿肋赤藓结皮AMF群落组成与多样性状况,尤其是降雪前和融雪期AMF群落结构差异。【结果】降雪前、雪盖期及融雪期检测到的OTU分属于球囊菌门(Glomeromycota)的5目9科11属,其中,近明球囊霉属(Claroideoglomus)、原囊霉属(Archaeospora)、类球囊霉属(Paraglomus)和球囊霉属(Glomus)为优势类群;降雪前和融雪期齿肋赤藓结皮层中绝对优势属(>50%)均为近明球囊霉属。群落丰富度Chao1指数和ACE指数均表现为雪盖前>积雪期>融雪期,表明降雪减少了AMF群落丰富度。近明球囊霉属融雪期比例大幅增加,而类球囊霉属、球囊霉属则较降雪前比例下降。基于MEGAN的分类学组成信息可视化分析表明,低丰度AMF类群更容易受到影响,无梗囊霉属(Acaulospora)主要集中在降雪前采集的样品中,而多样孢囊霉属(Diversispora)主要集中在融雪期样品中。结合聚类分析的属水平群落组成热图发现,高丰度分类单元的类别由降雪前的5种集中为2种。主成分分析结果表明,主成分1能够区分降雪前后的AMF群落结构特征,进一步验证降雪缺失对藓类结皮层AMF群落组成有筛选作用。高丰度优势属近明球囊霉属和球囊霉属之间、类球囊霉属和原囊霉属之间均呈现负相关,可能存在竞争关系;低丰度属巨孢囊霉属(Gigaspora)、隔球囊霉属(Septoglomus)、双型囊霉属(Ambispora)、盾巨孢囊霉属(Scutellospora)呈现正相关,可能存在协作关系以适应降雪。【结论】古尔班通古特沙漠的冬季降雪对苔藓结皮层AMF类群中的优势属和低丰度属有不同的选择策略。融雪期绝对优势属会降低存在竞争关系优势属的比例,进一步巩固优势地位,而存在正相关的低丰度属会同步降低比例,而且苔藓结皮层AMF优势属在该沙漠为近明球囊霉属。